2026-04-23 @ ALS 8.3.1
Overall Goals
- Liquid ethane vs liquid nitrogen cooling
- Check damage rates at 8.3.1 post flux calibration
Participants
- In person: Kara, Steve, James, Mehagan
Data
- Root directory at ALS:
/data/mcfuser/ucsf/fraser/23Apr2026/diffuse - Root directory on OSN:
s3://diffuse-als-public/20260423/
Beamline Settings
Day 1 Parameters — Cryo
| Parameter | Value | Notes |
|---|---|---|
| X-ray energy | 14000 eV @ 0.014 % bandwidth | |
| Beam size | 100 µm x 100 µm, circle | |
| Flux | 3.35 × 10¹¹ ph/s | 16.72 kGy/s |
| Beamstop | standard 8.3.1 | |
| Data collection software | Blu-Ice | |
| Temperature control | Cryo-stream, 100 K |
Samples
| Name | Sample | Well composition | Drop composition | Notes |
|---|---|---|---|---|
| Mac1 (P43) | SARS CoV2 NSP3 macrodomain and seed stock. 40 mg/mL Mac1 in 150 mM NaCl, 20 mM Tris pH 8, 5% glycerol | 34% (w/vol) PEG 3000 + 100 mM CHES (pH 9.5) | 200 nL protein solution + 100 nL well solution + 100 nL seeds | Kara setup. Reference PDB: 7kqo |
| Lysozyme | 20 mg/mL | 30% PEG 5000, 1 M NaCl, 0.05 M Na Acetate trihydrate pH 4.6 | Kara set up | |
| Mac1 (C2) | SARS CoV2 NSP3 macrodomain, 15 mg/mL Mac1 in 150 mM NaCl, 20 mM Tris pH 8, 5% glycerol | 100 mM Tris pH 8.5, 100 mM Na Acetate, 25–35% PEG 4000 | 200 nL protein solution + 200 nL well solution | Kara set up. Reference PDB: 7KR0 |
Data Collection — Cryo
Mac1 cryo ethane 1
Subdirectory: mac1/cryo_ethane
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_ethane_1 | 0 | 720 | 0.1 | 7200 | 0.1 | 200 | Was icy, tried to spray clean but it likely annealed during that, lots of ice rings. No bg — ∆t was accidentally too high |
Mac1 cryo ethane 2
Subdirectory: mac1/cryo_ethane
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_ethane_2 | 0 | 720 | 0.1 | 7200 | 0.01 | 200 | Saw nothing on detector — abort run and run tune up |
| mac1_cryo_ethane_2 | 0 | 720 | 0.1 | 7200 | 0.01 | 200 | Fixed, but still have ice rings |
Mac1 cryo ethane 3
Subdirectory: mac1/cryo_ethane
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_ethane_3 | 0 | 720 | 0.1 | 7200 | 0.01 | 200 | Ice, but different ice (hexagonal), had slipping — possibly loose pin. Try again |
| mac1_cryo_ethane_3 | 0 | 720 | 0.1 | 7200 | 0.01 | 200 | Fixed pin, still some ice, also nylon loop background |
Mac1 cryo ethane 4
Subdirectory: mac1/cryo_ethane
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_ethane_4 | 0 | 720 | 0.1 | 7200 | 0.01 | 200 | Loop more clear, but still some ice. Cubic this time. Least ice so far |
| mac1_cryo_ethane_bg_4 | 0 | 720 | 1 | 720 | 0.1 | 200 | ~240 µm away |
Xia2 processing: image range: [1, 1800], resolution (CC½ > 0.3): 0.93 Å, Wilson B: 8.0 Ų, mosaicity: nan, unit cell: a = 88.68 Å, c = 39.71 Å
Mac1 cryo ethane 5
Subdirectory: mac1/cryo_ethane
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_ethane_5 | 0 | 720 | 0.1 | 7200 | 0.01 | 200 | No ice rings, maybe a couple of ice spots. RAM filling up and weird rotation in the middle put crystal out of beam |
| mac1_cryo_ethane_5_2 | 0 | 720 | 1 | 7200 | 0.01 | 200 | Re-center and go again, RAM issue again |
| mac1_cryo_ethane_5_3 | 0 | 720 | 1 | 7200 | 0.01 | 200 | Worked well, still had rotation in between, just collect 360 |
| mac1_cryo_ethane_5_bg | 0 | 720 | 1 | 720 | 0.1 | 200 | Went 200 µm away |
Mac1 cryo ethane 6
Subdirectory: mac1/cryo_ethane
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_ethane_6 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Clean, no ice |
| mac1_cryo_ethane_bg_6 | 0 | 360 | 1 | 360 | 0.1 | 200 | Went ~200 µm away |
Xia2 processing: image range: [1, 3600], resolution (CC½ > 0.3): 0.99 Å, Wilson B: 10.37 Ų, mosaicity: 0.065, unit cell: a = 88.64 Å, c = 38.97 Å
Mac1 cryo ethane 7
Subdirectory: mac1/cryo_ethane
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_ethane_7 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Clean, no ice, crystal looked a little dirty but must be PEG |
| mac1_cryo_ethane_bg_7 | 0 | 360 | 1 | 360 | 0.1 | 200 | Went 200 µm away |
Xia2 processing: image range: [1, 3600], resolution (CC½ > 0.3): 1.07 Å, Wilson B: 9.57 Ų, mosaicity: 0.209, unit cell: a = 88.36 Å, c = 38.46 Å
Mac1 cryo ethane 8
Loop smashed, no crystal — skip
Mac1 cryo ethane 9
Subdirectory: mac1/cryo_ethane
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_ethane_9 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Data collection failed |
| mac1_cryo_ethane_9_2 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Minor ice |
| mac1_cryo_ethane_bg_9 | 0 | 360 | 1 | 360 | 0.1 | 200 | Went 200 µm away |
Mac1 cryo ethane 10
Subdirectory: mac1/cryo_ethane
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_ethane_10 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Super clean |
| mac1_cryo_ethane_bg_10 | 0 | 360 | 1 | 360 | 0.1 | 200 | Went 200 µm away |
Mac1 cryo ethane 11
Subdirectory: mac1/cryo_ethane
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_ethane_11 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Icy |
Mac1 cryo ethane 12
Dropped in the hutch — skip
Mac1 cryo ethane 13
Subdirectory: mac1/cryo_ethane
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_ethane_13 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Tried to go for non-icy edge, mostly missing it, just some weak diffraction |
| mac1_cryo_ethane_13_2 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Cleaner than expected given amount of stuff on crystal, couple extra stray spots |
| mac1_cryo_ethane_bg_13 | 0 | 360 | 1 | 360 | 0.1 | 200 | Went 200 µm away |
Mac1 cryo ethane 14
Super icy — skip
Mac1 cryo N2 1
Subdirectory: mac1/cryo_n2
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_n2_1 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Ice on edges |
| mac1_cryo_n2_bg_1 | 0 | 360 | 1 | 360 | 0.1 | 200 |
Mac1 cryo N2 2
Subdirectory: mac1/cryo_n2
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_n2_2 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Some light ice |
| mac1_cryo_n2_bg_2 | 0 | 360 | 1 | 360 | 0.1 | 200 |
Mac1 cryo N2 3
Subdirectory: mac1/cryo_n2
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_n2_3 | 0 | 180 | 0.1 | 1800 | 0.01 | 200 | Loop bent a bit, just collect 180, still some ice |
| mac1_cryo_n2_bg_3 | 0 | 180 | 1 | 180 | 0.1 | 200 | Went 150 µm away |
Mac1 cryo N2 4
Subdirectory: mac1/cryo_n2
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_n2_4 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Clean |
| mac1_cryo_n2_bg_4 | 0 | 360 | 1 | 360 | 0.1 | 200 | Went 300 µm away |
Xia2 processing: image range: [1, 3600], resolution (CC½ > 0.3): nan Å, Wilson B: 8.49 Ų, mosaicity: 0.089, unit cell: a = 88.67 Å, c = 39.69 Å
Mac1 cryo N2 5
Subdirectory: mac1/cryo_n2
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_n2_5 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Seems like 2 crystals stuck together |
| mac1_cryo_n2_5_2 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Went to tiny region with no overlap, getting cleaner, but weaker diffraction |
Mac1 cryo N2 6
Lots of ice and bent — skip
Mac1 cryo N2 7
Subdirectory: mac1/cryo_n2
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_n2_7 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Gave a quick wash, still very icy |
Mac1 cryo N2 8
Subdirectory: mac1/cryo_n2
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_n2_8 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Light ice |
| mac1_cryo_n2_bg_8 | 0 | 360 | 1 | 360 | 0.1 | 200 | Went 250 µm away |
Xia2 processing: image range: [1, 3600], resolution (CC½ > 0.3): nan Å, Wilson B: 8.14 Ų, mosaicity: 0.044, unit cell: a = 88.72 Å, c = 39.79 Å
Mac1 cryo N2 9
Very icy despite wash and anneal — skip
Mac1 cryo N2 10
Subdirectory: mac1/cryo_n2
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_n2_10 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Light ice |
| mac1_cryo_n2_bg_10 | 0 | 360 | 1 | 360 | 0.1 | 200 | Went 300 µm away |
Xia2 processing: image range: [1, 3600], resolution (CC½ > 0.3): 0.94 Å, Wilson B: 8.06 Ų, mosaicity: 0.064, unit cell: a = 88.68 Å, c = 39.75 Å
Mac1 cryo N2 11
Icy and crystal unclear — skip
Mac1 cryo N2 12
Subdirectory: mac1/cryo_n2
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_n2_12 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Ice, detector stopped |
| mac1_cryo_n2_12_2 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Go to slightly new spot and go again, still some ice |
| mac1_cryo_n2_bg_12 | 0 | 360 | 1 | 360 | 0.1 | 200 | Went 200 µm away |
Mac1 cryo N2 13
Subdirectory: mac1/cryo_n2
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_n2_13 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Very clean |
| mac1_cryo_n2_bg_13 | 0 | 360 | 1 | 360 | 0.1 | 200 | Went 300 µm away |
Xia2 processing: image range: [1, 3600], resolution (CC½ > 0.3): 0.93 Å, Wilson B: 7.95 Ų, mosaicity: 0.051, unit cell: a = 88.75 Å, c = 39.79 Å
Mac1 cryo N2 14
Subdirectory: mac1/cryo_n2
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_n2_14 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Some ice |
| mac1_cryo_n2_bg_14 | 0 | 360 | 1 | 360 | 0.1 | 200 | Went 300 µm away |
Mac1 cryo N2 15
Subdirectory: mac1/cryo_n2
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_n2_15 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Some ice, plus clumpy crystals/multi-lattice |
Mac1 cryo N2 16
Subdirectory: mac1/cryo_n2
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_cryo_n2_16 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Annealed, icy/unhappy |
Data Collection — Room Temperature
Beamline Settings — Day 1 RT
James lowered M1 divergence to 0.135 mrad to defocus the beam.
| Parameter | Value | Notes |
|---|---|---|
| X-ray energy | 14000 eV @ 0.014 % bandwidth | |
| Beam size | 100 µm x 100 µm, circle | |
| Flux | 1.87 × 10¹⁰ ph/s | Vertical defocus, 100% transmission — 935.6 Gy/s |
| Beamstop | standard 8.3.1 | |
| Data collection software | Blu-Ice | |
| Temperature control | off |
Mac1 apo 1
Kara looped a Mac1 P43 crystal in the humid box, cut a sleeve to length, added 10 µL of well solution in the tip. Custom sleeves still a bit too long, had to cut approximately ⅓ off.
Subdirectory: mac1/apo
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_apo_1 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Nice |
| mac1_apo_bg_1 | 0 | 360 | 1.0 | 360 | 0.1 | 200 |
Xia2 processing: image range: [1, 3600], resolution (CC½ > 0.3): 1.16 Å, Wilson B: 12.21 Ų, mosaicity: 0.017, unit cell: a = 89.16 Å, c = 40.16 Å
Mac1 apo 2
Kara looped a Mac1 P43 crystal in the humid box, re-used sleeve.
Subdirectory: mac1/apo
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_apo_2 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Nice |
| mac1_apo_bg_2 | 0 | 360 | 1.0 | 360 | 0.1 | 200 |
Xia2 processing: image range: [1, 3600], resolution (CC½ > 0.3): 1.13 Å, Wilson B: 12.34 Ų, mosaicity: 0.015, unit cell: a = 89.23 Å, c = 40.31 Å
Mac1 apo 3
Kara looped a Mac1 P43 crystal in the humid box, re-used sleeve.
Subdirectory: mac1/apo
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_apo_3 | 0 | 360 | 0.1 | 3600 | 0.01 | 200 | Nice |
| mac1_apo_bg_3 | 0 | 360 | 1.0 | 360 | 0.1 | 200 |
Xia2 processing: image range: [1, 3600], resolution (CC½ > 0.3): 1.15 Å, Wilson B: 12.13 Ų, mosaicity: 0.012, unit cell: a = 89.2 Å, c = 40.24 Å
Mac1 apo 4
Kara looped a Mac1 P43 crystal in the humid box, re-used sleeve. Played with exposure time; keeping max dose of 100 kGy in mind.
Subdirectory: mac1/apo
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_apo_4 | 0 | 360 | 0.1 | 3600 | 0.02 | 200 | Nice |
| mac1_apo_bg_4 | 0 | 360 | 1.0 | 360 | 0.2 | 200 | |
| mac1_apo_4_2 | 0 | 360 | 0.1 | 3600 | 0.02 | 200 | Repeat collection to check for damage |
| mac1_apo_4_2_bg | 0 | 360 | 1.0 | 360 | 0.2 | 200 |
Xia2 processing (mac1_apo_4): image range: [1, 3600], resolution (CC½ > 0.3): 1.09 Å, Wilson B: 12.29 Ų, mosaicity: 0.012, unit cell: a = 89.23 Å, c = 40.26 Å
Xia2 processing (mac1_apo_4_2): image range: [1, 3600], resolution (CC½ > 0.3): 1.15 Å, Wilson B: 12.66 Ų, mosaicity: 0.012, unit cell: a = 89.19 Å, c = 40.2 Å
Mac1 apo 5
Kara looped a Mac1 P43 crystal in the humid box, new sleeve with 10 µL well solution. Played with exposure time; keeping max dose of 100 kGy in mind.
Subdirectory: mac1/apo
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_apo_5 | 0 | 360 | 0.1 | 3600 | 0.03 | 200 | Nice |
| mac1_apo_bg_5 | 0 | 360 | 1.0 | 360 | 0.3 | 200 | |
| mac1_apo_5_2 | 0 | 360 | 0.1 | 3600 | 0.03 | 200 | Repeat collection to check for damage |
| mac1_apo_5_2_bg | 0 | 360 | 1.0 | 360 | 0.3 | 200 |
Xia2 processing (mac1_apo_5): image range: [1, 3600], resolution (CC½ > 0.3): 1.14 Å, Wilson B: 11.81 Ų, mosaicity: 0.022, unit cell: a = 89.2 Å, c = 40.16 Å
Xia2 processing (mac1_apo_5_2): image range: [1, 3600], resolution (CC½ > 0.3): 1.25 Å, Wilson B: 12.64 Ų, mosaicity: 0.018, unit cell: a = 89.17 Å, c = 40.08 Å
Lysozyme 1
Kara looped a lysozyme crystal in the humid box, new sleeve. Played with exposure time; keeping max dose of 100 kGy in mind.
Subdirectory: lysozyme
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| lysozyme_1 | 0 | 360 | 0.1 | 3600 | 0.02 | 200 | Nice |
| lysozyme_1_bg | 0 | 360 | 1.0 | 360 | 0.2 | 200 | |
| lysozyme_1_2 | 0 | 360 | 0.1 | 3600 | 0.02 | 200 | Repeat collection to check for damage |
| lysozyme_1_2_bg | 0 | 360 | 1.0 | 360 | 0.2 | 200 |
Indexing failed at beginning and end — likely due to crystal motion in the loop (Kara looped a lot of solvent with the crystal so it was floating a bit). Steve knows a fix using the local flag in dials.index (must be run manually, not with xia2):
dials.index imported.expt strong.refl space_group=P43212 indexing.index_assignment.method=local
Lysozyme 2
Kara looped a lysozyme crystal in the humid box, re-used sleeve (cut slightly to shorten). Played with exposure time; keeping max dose of 100 kGy in mind.
Subdirectory: lysozyme
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| lysozyme_2 | 0 | 360 | 0.1 | 3600 | 0.02 | 200 | Nice |
| lysozyme_2_bg | 0 | 360 | 1.0 | 360 | 0.2 | 200 |
Xia2 processing: image range: [1, 3600], resolution (CC½ > 0.3): 1.21 Å, Wilson B: 15.89 Ų, mosaicity: 0.049°, unit cell: a = 78.66 Å, c = 38.3 Å
Lysozyme 3
Kara looped a lysozyme crystal in the humid box, re-used sleeve.
Subdirectory: lysozyme
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| lysozyme_3 | 0 | 360 | 0.1 | 3600 | 0.02 | 200 | Nice |
| lysozyme_3_bg | 0 | 360 | 1.0 | 360 | 0.2 | 200 |
Xia2 processing: image range: [1, 3600], resolution (CC½ > 0.3): 1.2 Å, Wilson B: 15.62 Ų, mosaicity: 0.04, unit cell: a = 78.68 Å, c = 38.34 Å
End of Day 1. Takeaway from dose rate analysis: 20 ms exposure time works well at 360° and 720°. Stick to that for the rest. Vertical defocus working really well — replicate in the future.
Data Collection — Day 2 RT
Beamline Settings — Day 2 RT
Starting with SOS chip provided by ALS. Use Etnom 3 µm film.
| Parameter | Value | Notes |
|---|---|---|
| X-ray energy | 14000 eV @ 0.014 % bandwidth | |
| Beam size | 100 µm x 100 µm, circle | |
| Flux | 1.82 × 10¹⁰ ph/s | Vertical defocus, 100% transmission — 935.6 Gy/s |
| Beamstop | standard 8.3.1 | |
| Data collection software | Blu-Ice | |
| Temperature control | off |
Mac1 SOS 1
Load Mac1 from plate — crystals stuck to the well, so a bit hard to pipette up. After traveling around the chip, found one.
Subdirectory: mac1/sos_1
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_sos_1_1 | 175 | 185 | 0.1 | 100 | 0.3 | 200 | Chip did full rotation and hit microscope — abort. Test with pin to make sure everything is happy before repeating |
| mac1_sos_1_2 | 175 | 185 | 0.1 | 100 | 0.3 | 200 | Data collection not actually starting — troubleshoot and go. Diffraction looks nice. Crystal did not settle/move. Frame 1 did not get collected, starts at frame 2 |
| mac1_sos_1_2_bg | 175 | 185 | 1 | 10 | 3 | 200 | Background next to crystal |
Mac1 SOS 2
Load Mac1 from batch crystallization (Kara had leftover). Suspect the chip dried out — will check with unit cell parameters over time.
Subdirectory: mac1/sos_2
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_sos_2_1 | 175 | 185 | 0.1 | 100 | 0.3 | 200 | Crystal is a little uneven, but there is diffraction |
| mac1_sos_2_1_bg | 175 | 185 | 1 | 10 | 3 | 200 | |
| mac1_sos_2_2 | 175 | 185 | 0.1 | 100 | 0.3 | 200 | New crystal and new neighborhood |
| mac1_sos_2_3 | 175 | 185 | 0.1 | 100 | 0.3 | 200 | New crystal, same neighborhood |
| mac1_sos_2_2-3_bg | 175 | 185 | 1 | 10 | 3 | 200 | One background per neighborhood — this one is for crystals 2 and 3 |
| mac1_sos_2_4 | — | — | — | snapshot | — | — | No diffraction |
| mac1_sos_2_5 | 175 | 185 | 0.1 | 100 | 0.3 | 200 | New crystal and new neighborhood. Tiny crystal — weak diffraction |
| mac1_sos_2_6 | 175 | 185 | 0.1 | 100 | 0.3 | 200 | New crystal, same neighborhood, switch to 20 µm pinhole. Weak diffraction |
| mac1_sos_2_7 | 175 | 185 | 0.1 | 100 | 0.3 | 200 | New crystal, new neighborhood, switch to 50 µm pinhole. Go for larger crystals |
| mac1_sos_2_8 | 175 | 185 | 0.1 | 100 | 0.3 | 200 | New crystal, same neighborhood, stick with 50 µm pinhole |
| mac1_sos_2_9 | 175 | 185 | 0.1 | 100 | 0.3 | 200 | New crystal, same neighborhood, stick with 50 µm pinhole |
| mac1_sos_2_7-9_bg | 175 | 185 | 1 | 10 | 3 | 200 | One background per neighborhood — this one is for crystals 7, 8, and 9. Has a ring feature — from collimator? |
| mac1_sos_2_7-9_bg_100 | 175 | 185 | 1 | 10 | 3 | 200 | Re-take with 100 µm pinhole — ring still there |
| mac1_sos_2_10 | 175 | 185 | 0.1 | 100 | 0.3 | 200 | New crystal, new neighborhood. 100 µm pinhole |
| mac1_sos_2_11 | 175 | 185 | 0.1 | 100 | 0.3 | 200 | New crystal, same neighborhood. 100 µm pinhole |
| mac1_sos_2_12 | 175 | 185 | 0.1 | 100 | 0.3 | 200 | New crystal, same neighborhood. 100 µm pinhole |
| mac1_sos_2_13 | 175 | 185 | 0.1 | 100 | 0.3 | 200 | New crystal, same neighborhood. 100 µm pinhole |
| mac1_sos_2_14 | 175 | 185 | 0.1 | 100 | 0.3 | 200 | New crystal, same neighborhood. 100 µm pinhole |
| mac1_sos_2_10-14_bg | 175 | 185 | 1 | 10 | 3 | 200 | One background per neighborhood — this one is for crystals 10–14 |
Mac1 SOS 3
Load Mac1 from batch crystallization (Kara had leftover), different tube this time — crystals seem higher quality. Some crystals floating, but a lot held by the windows. Suspect the chip dried out — will check with unit cell parameters over time.
Subdirectory: mac1/sos_3
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_sos_3_1 | 160 | 220 | 0.1 | 600 | 0.1 | 200 | Carefully evaluated rotation range, can increase to ±30°, centered at 190°. Keep 100 µm pinhole |
| mac1_sos_3_2 | 160 | 220 | 0.1 | 600 | 0.1 | 200 | New crystal, same neighborhood |
| mac1_sos_3_3 | 160 | 220 | 0.1 | 600 | 0.1 | 200 | New crystal, same neighborhood |
| mac1_sos_3_4 | 160 | 220 | 0.1 | 600 | 0.1 | 200 | New crystal, same neighborhood |
| mac1_sos_3_5 | 160 | 220 | 0.1 | 600 | 0.1 | 200 | New crystal, same neighborhood |
| mac1_sos_3_1-5_bg | 160 | 220 | 1 | 60 | 1 | 200 | Background for this neighborhood |
| mac1_sos_3_6 | 160 | 220 | 0.1 | 600 | 0.1 | 200 | New crystal, new neighborhood. Had some rings in the beginning — maybe got too close at this new chip position. Abandon this neighborhood |
| mac1_sos_3_7 | 160 | 220 | 0.1 | 600 | 0.1 | 200 | New crystal, new neighborhood |
| mac1_sos_3_8 | 160 | 220 | 0.1 | 600 | 0.1 | 200 | New crystal, same neighborhood — bad run? some movement along rotation |
| mac1_sos_3_9 | 160 | 220 | 0.1 | 600 | 0.1 | 200 | New crystal, same neighborhood |
| mac1_sos_3_10 | 160 | 220 | 0.1 | 600 | 0.1 | 200 | New crystal, same neighborhood |
| mac1_sos_3_11 | 160 | 220 | 0.1 | 600 | 0.1 | 200 | New crystal, same neighborhood |
| mac1_sos_3_12 | 160 | 220 | 0.1 | 600 | 0.1 | 200 | New crystal, same neighborhood |
| mac1_sos_3_7-12_bg | 160 | 220 | 1 | 600 | 1 | 200 | Background for this neighborhood. Accidentally set to 600 images instead of 60, aborted after ~90 |
| mac1_sos_3_13 | 160 | 220 | 0.1 | 600 | 0.1 | 200 | New crystal, new neighborhood. First part of rotation has intense shadow. Abandon this neighborhood. Weird issue: run 2 was incomplete and it continued that run |
| mac1_sos_3_14 | 150 | 210 | 0.1 | 600 | 0.1 | 200 | New crystal, new neighborhood. Looking good |
| mac1_sos_3_15 | 150 | 210 | 0.1 | 600 | 0.1 | 200 | New crystal, same neighborhood |
| mac1_sos_3_16 | 150 | 210 | 0.1 | 600 | 0.1 | 200 | New crystal, same neighborhood — a little weak, probably skip |
| mac1_sos_3_17 | 150 | 210 | 0.1 | 600 | 0.1 | 200 | New crystal, same neighborhood |
| mac1_sos_3_18 | 150 | 210 | 0.1 | 600 | 0.1 | 200 | Shutter opened but gonio did not progress. Kill and skip this crystal |
| mac1_sos_3_14-17_bg | 150 | 210 | 1 | 60 | 1 | 200 | Background for this neighborhood. Failed to collect — detector hardware triggering problem |
| mac1_sos_3_14-17_bg | 150 | 210 | 1 | 60 | 1 | 200 | Re-collect |
Mac1 SOS 4
Collect just chip + film + grease to get background.
Mac1 apo 6
Kara looped a Mac1 P43 crystal in the humid box, new sleeve with 10 µL well solution.
Subdirectory: mac1/apo
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_apo_6 | 0 | 360 | 0.1 | 3600 | 0.02 | 200 | All good |
| mac1_apo_bg_6 | 0 | 360 | 1.0 | 360 | 0.2 | 200 | Went 200 µm away |
Mac1 opener 1
Kara made a drop with 4.5 µL reservoir + 0.5 µL of 100 mM opener and transferred two crystals to the drop. Looped the first Mac1 after ~1 hr; it cracked a little.
Subdirectory: mac1/opener
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_opener_1 | 0 | 360 | 0.1 | 3600 | 0.02 | 200 | All good — no obvious splitting in the spots |
| mac1_opener_1_bg | 0 | 360 | 1.0 | 360 | 0.2 | 200 | Went 200 µm away |
Mac1 apo 7
Kara looped a Mac1 P43 crystal in the humid box, new sleeve with 10 µL well solution.
Subdirectory: mac1/apo
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_apo_7 | 0 | 360 | 0.1 | 3600 | 0.02 | 200 | All good |
| mac1_apo_bg_7 | 0 | 360 | 1.0 | 360 | 0.2 | 200 | Went 300 µm away |
Mac1 apo 8
Kara looped a Mac1 P43 crystal in the humid box, re-used sleeve with 10 µL well solution.
Subdirectory: mac1/apo
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_apo_8 | 0 | 360 | 0.1 | 3600 | 0.02 | 200 | All good |
| mac1_apo_bg_8 | 0 | 360 | 1.0 | 360 | 0.2 | 200 | Went 300 µm away |
Mac1 opener 2
Kara made a drop with 4.5 µL reservoir + 0.5 µL of 100 mM opener and transferred two crystals to the drop. Looped the first Mac1 after ~2 hr; it cracked a lot, but grabbed a piece.
Subdirectory: mac1/opener
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_opener_2 | 0 | 360 | 0.1 | 3600 | 0.02 | 200 | No real diffraction |
Mac1 opener 3
Kara made a drop with 6.5 µL reservoir + 0.5 µL of 100 mM opener and transferred three crystals to the drop. Looped the first Mac1 after ~40 min; it cracked a lot, but grabbed a piece.
Subdirectory: mac1/opener
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_opener_3 | 0 | 360 | 0.1 | 3600 | 0.02 | 200 | Diffraction |
| mac1_opener_3_bg | 0 | 360 | 1 | 360 | 0.2 | 200 | Moved 200 µm away |
Mac1 opener 4
Kara made a drop with 6.5 µL reservoir + 0.5 µL of 100 mM opener and transferred three crystals to the drop. Looped the first Mac1 after ~60 min; it cracked a lot, but grabbed a piece.
Subdirectory: mac1/opener
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_opener_4 | 0 | 360 | 0.1 | 3600 | 0.02 | 200 | Diffraction and bent loop |
| mac1_opener_4_bg | 0 | 360 | 1 | 360 | 0.2 | 200 | Moved 200 µm away |
Mac1 opener 5
Kara made another drop with 6.5 µL reservoir + 0.5 µL of 100 mM opener and transferred three crystals to the drop. Looped the first Mac1 after ~30 min; it cracked a lot, but grabbed a piece.
Subdirectory: mac1/opener
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_opener_5 | 0 | 360 | 0.1 | 3600 | 0.02 | 200 | Diffraction and bent loop |
| mac1_opener_5_bg | 0 | 360 | 1 | 360 | 0.2 | 200 | Moved 200 µm away |