9HFY | pdb_00009hfy

Crystal structure of SARS CoV-2 3CLpro (Mpro) with ALG-097078

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Proprietary model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.25	293	PEG 2000 MME, Bis-Tris

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.283	α = 90
b = 99.039	β = 108.19
c = 59.08	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	100	PIXEL	DECTRIS EIGER X 16M		2020-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000040	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	1.282	56.128	94	0.037	0.037	0.02	0.999	15.9	4		145163

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.282	1.304	60.3		0.689	0.689	0.504	0.609	1.3	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.282	56.128	137965	7192	94.01	0.1736	0.1728	0.182	0.1896	0.1974	RANDOM	22.239

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]
-0.11		-0.61	-0.02		0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.979
r_dihedral_angle_3_deg	13.588
r_dihedral_angle_4_deg	11.801
r_dihedral_angle_1_deg	6.741
r_mcangle_it	3.361
r_mcbond_it	2.45
r_mcbond_other	2.435
r_angle_refined_deg	1.704
r_angle_other_deg	1.366
r_chiral_restr	0.104

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.979
r_dihedral_angle_3_deg	13.588
r_dihedral_angle_4_deg	11.801
r_dihedral_angle_1_deg	6.741
r_mcangle_it	3.361
r_mcbond_it	2.45
r_mcbond_other	2.435
r_angle_refined_deg	1.704
r_angle_other_deg	1.366
r_chiral_restr	0.104
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4698
Nucleic Acid Atoms
Solvent Atoms	638
Heterogen Atoms	96

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
XDS	data reduction
Aimless	data scaling
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.