7N8C

Joint X-ray/neutron structure of SARS-CoV-2 main protease (Mpro) in complex with Mcule5948770040

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7LTJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	18% PEG3350, 0.1 M Bis-Tris pH 7.0 reservoir solution and 0.2 microL microseeds at 1:200 dilution

Crystal Properties
Matthews coefficient	Solvent content
2.93	57.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.314	α = 90
b = 81.301	β = 96.46
c = 88.578	γ = 90

Symmetry
Space Group	I 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS EIGER R 4M	OSMIC VARIMAX	2021-03-10	M	SINGLE WAVELENGTH
2	1	neutron	293	AREA DETECTOR	ORNL ANGER CAMERA	COLLIMATORS	2021-03-03	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54
2	SPALLATION SOURCE	ORNL Spallation Neutron Source BEAMLINE MANDI	2.00-4.16	ORNL Spallation Neutron Source	MANDI

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.2	59.72	96.3	0.107			0.055	0.992		11.4	4.7		19108
2	2.5	12.86	85.6	0.212			0.096	0.946		15.6	5.5		11534

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.27		0.602				0.686		1.6	4.8
2	2.5	2.59		0.283						5.8	5.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	2.2	25.9		2.5		17476	856	88.1			0.177	0.192	RANDOM	44.13
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.5	12.86		2.5		11532	577	84.9			0.187	0.211	RANDOM	44.13

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
x_torsion_deg	27.1
x_torsion_deg	27.1
x_angle_deg	1.1
x_angle_deg	1.1
x_torsion_impr_deg	0.86
x_torsion_impr_deg	0.86
x_bond_d	0.008
x_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2368
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	24

Software

Software
Software Name	Purpose
nCNS	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHASER	phasing
nCNS	phasing
Mantid	data reduction
LAUENORM	data scaling

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.