6ZRU | pdb_00006zru

Crystal structure of SARS CoV2 main protease in complex with inhibitor Boceprevir

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6LU7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.75	291	100 mM MES pH 6.75 5% DMSO (V/V) 16% PEG 6000 (W/V) 300 uM Boceprevir

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.763	α = 90
b = 53.535	β = 101.52
c = 45.876	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	100	PIXEL	PSI PILATUS 6M		2020-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033200	PETRA III, DESY	P11

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	2.1	48.26	100	0.04	0.044	0.017	1	23.9	6.8		15941

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	2.1	2.16	100		0.702	0.758	0.284	0.83		7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6LU7	2.1	44.96	15173	766	99.97	0.189	0.1876	0.19	0.2154	0.22	RANDOM	50.982

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]
1.66		0.12	-0.4		-1.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.866
r_dihedral_angle_3_deg	15.073
r_dihedral_angle_4_deg	13.524
r_dihedral_angle_1_deg	8.117
r_angle_refined_deg	1.654
r_angle_other_deg	1.325
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.866
r_dihedral_angle_3_deg	15.073
r_dihedral_angle_4_deg	13.524
r_dihedral_angle_1_deg	8.117
r_angle_refined_deg	1.654
r_angle_other_deg	1.325
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2340
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	45

Software

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

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.