9HFX | pdb_00009hfx

Crystal structure of SARS CoV-2 3CLpro (Mpro) with ALG-097558

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	293	PCB, PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.312	α = 90
b = 53.102	β = 103.3
c = 45.613	γ = 90

Symmetry
Space Group	C 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	DECTRIS EIGER X 16M		2022-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.999992	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	1.959	55.623	94.5	0.098	0.098	0.059	0.996	7.8	3.6		18236

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	1.959	1.993	99.9		0.989	0.989	0.587	0.517	1.4	3.8

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	1.96	55.62	16388	1843	94.43	0.2147	0.2114	0.2153	0.243	0.2489	RANDOM	35.709

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]
1.31		-0.43	-0.04		-0.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.249
r_dihedral_angle_4_deg	17.335
r_dihedral_angle_3_deg	11.942
r_dihedral_angle_1_deg	6.399
r_mcangle_it	2.207
r_mcbond_it	1.292
r_mcbond_other	1.292
r_angle_refined_deg	1.208
r_angle_other_deg	0.957
r_chiral_restr	0.069

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.249
r_dihedral_angle_4_deg	17.335
r_dihedral_angle_3_deg	11.942
r_dihedral_angle_1_deg	6.399
r_mcangle_it	2.207
r_mcbond_it	1.292
r_mcbond_other	1.292
r_angle_refined_deg	1.208
r_angle_other_deg	0.957
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2347
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	45

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.