2026-09-30 @ CHESS 7b2

Under Construction

This page was auto-transcribed from handwritten notebooks and log files. We are currently reviewing for correctness and adding missing information (see TODO comments in markdown source). Use with caution.

First CHESS beam time of the 2026-3 run cycle.

Goals

Beamline alignment and optimization after summer upgrades
DHFR-Fol-NADP crystals from new batch: complete diffuse map at ambient temperature
RT diffraction from Mac1 grown from alternate crystallization procedures (Katie L's crystals).

Participants

Steve M, Neti B, and Katie L (main), Stephen T and Supratik G (learning) from Ando lab; support from Mike P, Mike C, John I, and Tricia C at CHESS.

Data

Root directory at CHESS: /nfs/chess/raw/2026-3/id7b2/meisburger/20260930

Root directory on OSN: s3://diffuse-chess-public/20260930

Beamline setup

parameter	value	notes
X-ray energy	14 keV @ 0.01% bandwidth	Si 111 channel cut mono inserted
Beam size	100 µm x 100 µm (initially)	Slit-defined, no CRL. Adjusted to match crystal size when noted, below.
Flux	3.9 x 10¹⁰ ph/s	ICol ~17,700 / 0.1 s; see SPEC `ct` output below
Background reduction	On-axis mirror with Mo tube
Centering camera	on-axis camera	New long working distance camera. Scalebar in screenshots (green bar, lower left) is 100 µm.
Beamstop	700 µm diameter Mo disk suspended on mylar sheet	semi-transparent
Data collection software	"MX Collect" (python) & SPEC	Modified by Mike P to handle the new camera
Temperature control	none (ambient)

Steve M, Steve T, Neti B, Mike P, Mike C, and Tricia C arrived between 9 and 10 am on September 30 to align the station. No significant bumping or cave optics adjustments were needed. However, a lot of things changed in the hutch over the summer, and in-hutch alignment was tricky. Getting beam through the channel cut, CRL pass-through, slits, and cleanup aperture turned out to be pretty difficult. Our hope was to begin data collection at noon, but alignment took all day; Mike P and Steve M stayed until midnight to finish. So data collection did not begin until October 1.

One new item is the centering camera. We previously were able to automatically save camera images at certain angles (every 30˚). This has not been implemented yet for the new camera, so we resorted to screenshots instead.

Samples

Name	Sample	Well composition	Notes
Lysozyme	Hen egg lysozyme, 50 mg/mL in NaOAc		24-well hanging-drop vapor diffusion tray set up by Supratik G for practice.
DHFR-Folate-NADP	E. coli dihydrofolate reductase expressed and purified at Cornell. Dialyzed in 20 mM imidazole pH 7.0 with 1 mM folic acid and concentrated to 35 mg/mL. NADP+ added in 3:1 molar excess (final concentrations: 31.5 mg/mL DHFR, 6.3 mM NADP)	15-18% PEG 400, 100 mM MnCl₂, 20 mM imidazole pH 7.0	Crystals were looped in the cold room under red light and transported to CHESS at 4 deg C. See Neti B's Notebook
Mac1 (P4₃)	SARS CoV2 NSP3 macrodomain	Several conditions from Katie L's optimization trays (see notes)	Trays named in the notebook: "Index H11 phase diagram" (wells G12, D11), "Index H11 new optimization" (wells D12, D?5), "Index H12 diagram" (well G12), and PEGRx F5 (well ?5). Crystals mac1_2 onward were looped in a humidity chamber.

Data collection

Steve M and Neti B arrived at the beamline at 8:15 on October 1. Katie L and Supratik G arrived later. The plan was to collect DHFR data in the morning, before handing off the beamline to Raley at noon (Raley has the non-diffuse beamtime after ours), and to request more time later for Mac1 experiments.

Steve tuned mono, mith, and upz, then locked in beam position feedback. He measured flux using the ion chamber (I2), see table above:

From id7b2.classe.cornell.edu
Thu Oct 01 08:44:50 2026

Output of macro ct           (14 keV, no atten, no CRL, slits 100 x 100)

Thu Oct 01 08:44:51 2026

     Seconds = 1
       Diode = 42 (42/s)
          I2 = 46016 (46016/s)       @ 50 nA/V
        ICol = 177142 (177142/s)
        Gate = 0 (0/s)
       QuadX = 0 (0/s)
       QuadY = 0.00013 (0.00013/s)
       newI1 = 146197 (146197/s)
       newI0 = 249982 (249982/s)

The flux is down from last run (9.7 x 10¹⁰ ph/s on 2026-06-22) by about 2.5x. Probably the focusing mirror or cave optics need attention. But it's plenty of flux for now. We will run without attenuation.

Collected a 1 s exposure with nothing in the beam to double-check the beamstop position and document the background scatter. Slits set to 100 x 100 µm.

Subdirectory: setup

prefix	φ0 (deg.)	∆φ (deg.)	images	∆t (s)	tf (%)	d (mm)	E (keV)
air_656	0	0	1	1	100	185	14

Looks great!

1. Lysozyme (dose test)

Neti looped a ~100 µm lysozyme crystal from Supratik's tray, well A1. Slits 100 x 100 µm.

Subdirectory: lysozyme

prefix	φ0 (deg.)	φ1 (deg.)	∆φ (deg.)	images	∆t (s)	tf (%)	d (mm)	E (keV)
lys_1_657	0	360	0.1	3600	0.03	100	185	14
lys_1_bg_658	0	360	1	360	0.3	100	185	14

multiple lattices

The well was crowded with small crystals, and evidently there are multiple in the loop (55% indexed). Not a useful diffuse dataset, but fine for checking radiation damage.

Processing with xia2: mosaicity 0.018˚, 55% indexed. B-factor decay is about 5 Å² per 180˚, or 0.1 Å² / second. So, tolerable dose limit is ~20 s at this flux. This is a bit higher than expected. Let's repeat with a fresh crystal at 0.01 second exposures.

xia2 processing

	lys_1_657
scan	657
Mosaic spread	0.018
Resolution	1.26
Unit Cell	[79.49, 79.49, 38.04, 90.0, 90.0, 90.0]
Image range	[1, 3600]
Completeness	100.0
Multiplicity	25.3
I/sigma	15.0
Rpim	0.019
Wilson B factor	20.04
Space group	P 43 21 2

2. Lysozyme (dose test, repeat)

Neti looped a ~50 µm lysozyme crystal from Supratik's tray, well B1. Slits 100 x 100 µm.

Subdirectory: lysozyme

prefix	φ0 (deg.)	φ1 (deg.)	∆φ (deg.)	images	∆t (s)	tf (%)	d (mm)	E (keV)
lys_2_659	0	360	0.1	3600	0.01	100	185	14
lys_2_bg_660	0	360	1	360	0.1	100	185	14

directory naming

Both lysozyme crystals (lys_1 and lys_2) were saved directly in lysozyme, without a per-crystal subdirectory. This differs from the DHFR samples below and from the later lysozyme crystal (lysozyme/Lys_steve_T).

xia2 processing

	lys_2_659
scan	659
Mosaic spread	0.007
Resolution	1.36
Unit Cell	[79.44, 79.44, 38.04, 90.0, 90.0, 90.0]
Image range	[1, 3600]
Completeness	100.0
Multiplicity	26.3
I/sigma	8.8
Rpim	0.034
Wilson B factor	20.16
Space group	P 43 21 2

setup change

To avoid damaging folate, we turned off all lights in the hutch and used amber light from the microscope for centering.

3. DHFR-Folate-NADP

DHFR_1_A1

Neti mounted DHFR crystal #1 (from well A1).

Slits changed to 50 x 50 µm. Vector scan along the length of the crystal (spinx translation: 246.4 µm).

Subdirectory: DHFR/DHFR_1_A1

Neti saved a screenshot in the same directory to show what the crystal looked like.

prefix	φ1 (deg.)	∆φ (deg.)	images	∆t (s)	tf (%)	d (mm)	E (keV)
DHFR_1_A1_661*	360	0.1	3600	0.01	100	999	14
DHFR_1_A1_662	360	0.1	3600	0.01	100	185	14
DHFR_1_A1_bg_663	360	1	360	0.1	100	185	14

incomplete dataset

* DHFR_1_A1_661: forgot to move the detector in (d = 999 mm). Closed the shutter after a few seconds to avoid damaging the crystal. Repeated the collection with the correct detector distance (DHFR_1_A1_662). Do not use scan 661. Note that the crystal received a few seconds of extra dose before scan 662.

file naming

The screenshot for this crystal is named DHFR_A1.png (no crystal number), unlike the later screenshots (DHFR_3_A2.png, etc.).

xia2 processing

	DHFR_1_A1_662
scan	662
Mosaic spread	0.048
Resolution	1.4
Unit Cell	[34.43, 45.73, 99.31, 90.0, 90.0, 90.0]
Image range	[1, 3600]
Completeness	100.0
Multiplicity	13.3
I/sigma	6.4
Rpim	0.071
Wilson B factor	18.19
Space group	P 21 21 21

4. DHFR-Folate-NADP

Neti mounted DHFR crystal #2 (from well A2). The crystal is sitting on the neck of the loop (not good for diffuse). No screenshot was recorded.

Slits 50 x 50 µm. Vector scan (spinx translation: 217.6 µm).

Subdirectory: DHFR/DHFR_2_A2

prefix	φ0 (deg.)	φ1 (deg.)	∆φ (deg.)	images	∆t (s)	tf (%)	d (mm)	E (keV)
DHFR_2_A2_664	0	360	0.1	3600	0.01	100	185	14
DHFR_2_A2_bg_665	0	360	1	360	0.1	100	185	14

crystal on the neck of the loop

Loop material is likely in the beam path, so this dataset is not ideal for diffuse scattering. Statistics are also somewhat poorer than the other DHFR crystals (Rpim 0.107, resolution 1.53 Å).

xia2 processing

	DHFR_2_A2_664
scan	664
Mosaic spread	0.023
Resolution	1.53
Unit Cell	[34.38, 45.47, 99.51, 90.0, 90.0, 90.0]
Image range	[1, 3600]
Completeness	100.0
Multiplicity	13.2
I/sigma	8.5
Rpim	0.107
Wilson B factor	21.17
Space group	P 21 21 21

5. DHFR-Folate-NADP

DHFR_3_A2

Neti mounted DHFR crystal #3 (from well A2). The crystal is sitting on the tip of the loop.

Slits 50 x 50 µm. Vector scan (spinx translation: 255.9 µm).

Subdirectory: DHFR/DHFR_3_A2

Neti saved a screenshot in the same directory.

prefix	φ0 (deg.)	φ1 (deg.)	∆φ (deg.)	images	∆t (s)	tf (%)	d (mm)	E (keV)
DHFR_3_A2_666	0	360	0.1	3600	0.01	100	185	14
DHFR_3_A2_bg_667	0	360	1	360	0.1	100	185	14

xia2 processing

	DHFR_3_A2_666
scan	666
Mosaic spread	0.026
Resolution	1.41
Unit Cell	[34.38, 45.6, 99.37, 90.0, 90.0, 90.0]
Image range	[1, 3600]
Completeness	99.5
Multiplicity	13.4
I/sigma	6.3
Rpim	0.057
Wilson B factor	18.73
Space group	P 21 21 21

6. DHFR-Folate-NADP

DHFR_4_A2

Neti mounted another DHFR crystal (#4, from well A2).

Slits 50 x 50 µm. Vector scan (spinx translation: 228.9 µm).

Subdirectory: DHFR/DHFR_4_A2

Neti saved a screenshot in the same directory.

prefix	φ0 (deg.)	φ1 (deg.)	∆φ (deg.)	images	∆t (s)	tf (%)	d (mm)	E (keV)
DHFR_4_A2_668	0	360	0.1	3600	0.01	100	185	14
DHFR_4_A2_bg_669	0	360	1	360	0.1	100	185	14

weak start of dataset

Very few spots at the beginning of the dataset. It needs to be truncated and refit. The xia2 result below used the full image range.

xia2 processing

	DHFR_4_A2_668
scan	668
Mosaic spread	0.03
Resolution	1.51
Unit Cell	[34.39, 45.45, 99.52, 90.0, 90.0, 90.0]
Image range	[1, 3600]
Completeness	100.0
Multiplicity	13.2
I/sigma	7.0
Rpim	0.072
Wilson B factor	20.78
Space group	P 21 21 21

7. DHFR-Folate-NADP

DHFR_5_A2

Neti mounted DHFR crystal #5 (from well A2).

Slits 50 x 50 µm. Vector scan (spinx translation: 235.2 µm).

Subdirectory: DHFR/DHFR_5_A2

Neti saved a screenshot in the same directory.

prefix	φ0 (deg.)	φ1 (deg.)	∆φ (deg.)	images	∆t (s)	tf (%)	d (mm)	E (keV)
DHFR_5_A2_670	0	360	0.1	3600	0.01	100	185	14
DHFR_5_A2_bg_671	0	360	1	360	0.1	100	185	14

poor statistics

Rpim is 0.204, about 2–4x higher than the other DHFR crystals collected today (0.049–0.107), despite similar resolution and I/sigma. Check processing (e.g. multiple lattices, indexing rate, or a problem partway through the scan) before using this dataset.

xia2 processing

	DHFR_5_A2_670
scan	670
Mosaic spread	0.023
Resolution	1.47
Unit Cell	[34.41, 45.52, 99.47, 90.0, 90.0, 90.0]
Image range	[1, 3600]
Completeness	100.0
Multiplicity	13.1
I/sigma	8.6
Rpim	0.204
Wilson B factor	19.92
Space group	P 21 21 21

8. DHFR-Folate-NADP

DHFR_6_A2

Neti mounted DHFR crystal #6 (from well A2).

Slits changed to 50 µm (height) x 120 µm (width), per notebook. Regular (not vector) scan.

Subdirectory: DHFR/DFHR_6_A2

Saved a screenshot in the same directory.

prefix	φ0 (deg.)	φ1 (deg.)	∆φ (deg.)	images	∆t (s)	tf (%)	d (mm)	E (keV)
DHFR_6_A2_672	0	360	0.1	3600	0.01	100	185	14
DHFR_6_A2_bg_673	0	360	1	360	0.1	100	185	14

directory name typo

The subdirectory was accidentally named DHFR/DFHR_6_A2 (should be DHFR/DHFR_6_A2). File prefixes are correct (DHFR_6_A2_*).

xia2 processing

	DHFR_6_A2_672
scan	672
Mosaic spread	0.019
Resolution	1.33
Unit Cell	[34.42, 45.58, 99.42, 90.0, 90.0, 90.0]
Image range	[1, 3600]
Completeness	100.0
Multiplicity	13.3
I/sigma	9.8
Rpim	0.049
Wilson B factor	17.01
Space group	P 21 21 21

9. DHFR-Folate-NADP

Neti mounted a funky looking crystal (#7, from well B4). It has "split ends", so we shot from the middle only. No screenshot was recorded.

Slits changed to 100 µm (height) x 150 µm (width), per notebook. Regular (not vector) scan.

Subdirectory: DHFR/DHFR_7_B4

prefix	φ0 (deg.)	φ1 (deg.)	∆φ (deg.)	images	∆t (s)	tf (%)	d (mm)	E (keV)
DHFR_7_B4_674	0	360	0.1	3600	0.01	100	185	14

poor diffraction

Poor diffraction. The background scan was skipped, and no xia2 processing results are available.

10. Lysozyme

Steve T looped another lysozyme crystal from well A2 of Supratik's tray. Slits 100 x 100 µm.

Subdirectory: lysozyme/Lys_steve_T

prefix	φ0 (deg.)	φ1 (deg.)	∆φ (deg.)	images	∆t (s)	tf (%)	d (mm)	E (keV)
Lys_A2_675	0	360	0.1	3600	0.01	100	185	14
Lys_A2_bg_676	0	360	1	360	0.1	100	185	14

directory and file naming

This crystal does not follow the naming convention used earlier in the day. The subdirectory is named after the person (lysozyme/Lys_steve_T; written as Lys-Steve_T in the notebook), and the prefix Lys_A2 uses a capital L and the well name instead of a crystal number (lys_1 and lys_2 above; this would have been lys_3).

We handed off the beamline to Raley S. at noon for her scheduled beamtime (under a different proposal). We will use extra time for Mac1 if Raley finishes early.

Katie L and Neti B returned at 8:00 pm to collect Mac1.

11. Mac1 (P4₃)

mac1_1

Katie looped the bigger crystal from the "Index H11 phase diagram" tray, well G12. Slits 100 x 100 µm.

Subdirectory: mac1/mac1_1

prefix	φ0 (deg.)	φ1 (deg.)	∆φ (deg.)	images	∆t (s)	tf (%)	d (mm)	E (keV)
mac1_1_684	0	360	0.1	3600	0.01	100	185	14
mac1_1_bg_685	0	360	1	360	0.1	100	185	14

lower completeness, higher mosaicity

Completeness is 90.2% and mosaic spread 0.071˚, compared with 95.9–100% and 0.012–0.042˚ for the other Mac1 crystals today.

xia2 processing

	mac1_1_684
scan	684
Mosaic spread	0.071
Resolution	1.06
Unit Cell	[89.4, 89.4, 40.29, 90.0, 90.0, 90.0]
Image range	[1, 3600]
Completeness	90.2
Multiplicity	11.2
I/sigma	14.1
Rpim	0.019
Wilson B factor	12.59
Space group	P 43

12. Mac1 (P4₃)

mac1_2

Katie looped a crystal in the humidity chamber, from the "Index H11 phase diagram" tray, well D11. The crystal had cracked in half; this half was easier to grab. Slits 100 x 100 µm.

Subdirectory: mac1/mac1_2

prefix	φ1 (deg.)	∆φ (deg.)	images	∆t (s)	tf (%)	d (mm)	E (keV)
mac1_2_686	360	0.1	3600	0.01	100	185	14
mac1_2_bg_687*	360	1	360	0.1	100	185	14
mac1_2_bg_fr_688	360	1	360	0.1	100	185	14

bad background scan

* mac1_2_bg_687: the crystal was still in the beam path, so this "background" is an overexposed crystal dataset, not a background. Diffraction still looked very good. Use mac1_2_bg_fr_688 as the background for mac1_2. Note also that the crystal received an extra 36 s of exposure after the data scan.

xia2 processing

	mac1_2_686
scan	686
Mosaic spread	0.021
Resolution	1.07
Unit Cell	[89.51, 89.51, 40.69, 90.0, 90.0, 90.0]
Image range	[1, 3600]
Completeness	95.9
Multiplicity	10.8
I/sigma	17.0
Rpim	0.015
Wilson B factor	13.25
Space group	P 43

13. Mac1 (P4₃)

mac1_3

Katie looped the second half of the cracked crystal from mac1_2 ("Index H11 phase diagram" tray, well D11) in the humidity chamber. Slits 100 x 100 µm.

Subdirectory: mac1/mac1_3

prefix	φ0 (deg.)	φ1 (deg.)	∆φ (deg.)	images	∆t (s)	tf (%)	d (mm)	E (keV)
mac1_3_689	0	360	0.1	3600	0.01	100	185	14
mac1_3_bg_690	0	360	1	360	0.1	100	185	14

xia2 processing

	mac1_3_689
scan	689
Mosaic spread	0.035
Resolution	1.14
Unit Cell	[89.51, 89.51, 40.71, 90.0, 90.0, 90.0]
Image range	[1, 3600]
Completeness	100.0
Multiplicity	11.9
I/sigma	14.5
Rpim	0.022
Wilson B factor	13.54
Space group	P 43

14. Mac1 (P4₃)

mac1_4

Katie looped a crystal in the humidity chamber, from the "Index H11 new optimization" tray, well D12, using a 300 µm loop. The crystal sits on the edge of the loop. Slits 100 x 100 µm.

Subdirectory: mac1/mac1_4

prefix	φ0 (deg.)	φ1 (deg.)	∆φ (deg.)	images	∆t (s)	tf (%)	d (mm)	E (keV)
mac1_4_691	0	360	0.1	3600	0.01	100	185	14
mac1_4_bg_692	0	360	1	360	0.1	100	185	14

xia2 processing

	mac1_4_691
scan	691
Mosaic spread	0.017
Resolution	1.06
Unit Cell	[89.51, 89.51, 40.55, 90.0, 90.0, 90.0]
Image range	[1, 3600]
Completeness	96.6
Multiplicity	10.5
I/sigma	16.1
Rpim	0.016
Wilson B factor	12.92
Space group	P 43

15. Mac1 (P4₃)

mac1_5

Neti looped a crystal in the humidity chamber, from the "Index H11 new optimization" tray. Slits 100 x 100 µm.

Subdirectory: mac1/mac1_5

prefix	φ0 (deg.)	φ1 (deg.)	∆φ (deg.)	images	∆t (s)	tf (%)	d (mm)	E (keV)
mac1_5_693	0	360	0.1	3600	0.01	100	185	14
mac1_5_bg_694	0	360	1	360	0.1	100	185	14

weaker data

I/sigma is 9.4 and Rpim 0.032, versus 14–17 and 0.015–0.022 for the other Mac1 crystals today.

xia2 processing

	mac1_5_693
scan	693
Mosaic spread	0.012
Resolution	1.13
Unit Cell	[89.45, 89.45, 40.37, 90.0, 90.0, 90.0]
Image range	[1, 3600]
Completeness	99.3
Multiplicity	11.7
I/sigma	9.4
Rpim	0.032
Wilson B factor	13.05
Space group	P 43

16. Mac1 (P4₃)

mac1_6

Katie looped a crystal in the humidity chamber, from the "Index H12 diagram" tray, well G12, using a 300 µm loop. Slits changed to 150 x 150 µm. We took two datasets at two different positions on the same crystal (regular, not vector, scans), with one shared background.

Subdirectory: mac1/mac1_6

prefix	φ1 (deg.)	∆φ (deg.)	images	∆t (s)	tf (%)	d (mm)	E (keV)
mac1_6_695	360	0.1	3600	0.01	100	185	14
mac1_6_2_696	360	0.1	3600	0.01	100	185	14
mac1_6_bg_697	360	1	360	0.1	100	185	14

two datasets, one crystal

mac1_6_2_696 is a second dataset on the same crystal at a different position, not a separate crystal. Both datasets share the background mac1_6_bg_697. The background was collected after both data scans, so it reflects the crystal's state after two full datasets. The two positions are not recorded in the scan log (regular scans).

xia2 processing

	mac1_6_695	mac1_6_2_696
scan	695	696
Mosaic spread	0.042	0.017
Resolution	1.08	1.07
Unit Cell	[89.48, 89.48, 40.42, 90.0, 90.0, 90.0]	[89.48, 89.48, 40.39, 90.0, 90.0, 90.0]
Image range	[1, 3600]	[1, 3600]
Completeness	97.8	97.0
Multiplicity	10.9	10.7
I/sigma	14.6	16.5
Rpim	0.019	0.017
Wilson B factor	12.94	12.85
Space group	P 43	P 43

17. Mac1 (P4₃)

mac1_7

Katie looped a crystal in the humidity chamber, from the PEGRx F5 tray. Slits 150 x 150 µm. Vector scan (spinx translation: 252.8 µm).

Subdirectory: mac1/mac1_7

prefix	φ0 (deg.)	φ1 (deg.)	∆φ (deg.)	images	∆t (s)	tf (%)	d (mm)	E (keV)
mac1_7_698	0	360	0.1	3600	0.01	100	185	14
mac1_7_bg_699	0	360	1	360	0.1	100	185	14

Done!

2026-09-30 @ CHESS 7b2

Goals

Participants

Data

Beamline setup

Samples

Data collection

1. Lysozyme (dose test)

2. Lysozyme (dose test, repeat)

3. DHFR-Folate-NADP

4. DHFR-Folate-NADP

5. DHFR-Folate-NADP

6. DHFR-Folate-NADP

7. DHFR-Folate-NADP

8. DHFR-Folate-NADP

9. DHFR-Folate-NADP

10. Lysozyme

11. Mac1 (P43)

12. Mac1 (P43)

13. Mac1 (P43)

14. Mac1 (P43)

15. Mac1 (P43)

16. Mac1 (P43)

17. Mac1 (P43)

Comments

11. Mac1 (P4₃)

12. Mac1 (P4₃)

13. Mac1 (P4₃)

14. Mac1 (P4₃)

15. Mac1 (P4₃)

16. Mac1 (P4₃)

17. Mac1 (P4₃)