Experiment: 7MBG

SARS-CoV-2 Main protease in orthorhombic space group

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5RGQ	PDB entry 5RGQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.1 M MES, pH 6.7, 5% v/v DMSO, 8% w/v PEG4000, 30% w/v PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.25	α = 90
b = 98.16	β = 90
c = 102.26	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2021-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9120	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.86	67.25	99.6	0.176	0.191	0.074	0.996	7.2	6.6		57312

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.91	99.2		3.084	3.341	1.278	0.314		6.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 5RGQ	1.86	56.19	1.34	57213	2914	99.4	0.1963	0.1949	0.1957	0.2221	0.2245	37.0014

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4669
Nucleic Acid Atoms
Solvent Atoms	353
Heterogen Atoms	56

Software

Software
Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing