7SUC

XFEL Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3M1V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.55	300	18% PEG 400, 150mM Mg Acetate, 100mM HEPES (pH 7.5)

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.082	α = 90
b = 119.777	β = 91.73
c = 123.21	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	300	CCD	RAYONIX MX340-HS		2020-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE MFX	1.3007	SLAC LCLS	MFX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	Drop On Tape	injection

Injection
Diffraction ID	Description	Flow Rate	Injector Diameter	Injection Power	Injector Nozzle	Filter Size	Carrier Solvent
1	Crystal slurry is injected onto a kapton tape from an acoustic droplet injector (ADE). The drop travels on the tape towards the X-ray interaction point where it is hit by the XFEL beam. This is the Drop-On-Tape (DOT) sample delivery system used by our team previously.						mother liquor

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	30	30	16	9.5

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Total Frames
1		24589	73742

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (All)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.9	21.25	99.91	0.979	0.515	3.356	41.43		189345			26.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93	99.82		0.379	0.831	0.696	9.89

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3M1V	1.9	21.25	1.34	188906	2008	99.84	0.1528	0.1524	0.1863	30.52

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.3826
f_angle_d	0.8169
f_chiral_restr	0.0464
f_plane_restr	0.0069
f_bond_d	0.0044

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19098
Nucleic Acid Atoms
Solvent Atoms	734
Heterogen Atoms	195

Software

Software
Software Name	Purpose
PHENIX	refinement
cctbx.xfel	data reduction
cxi.merge	data scaling
Coot	model building
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.