7SGU | pdb_00007sgu

Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder608 inhibitor

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	0.1 M sodium acetate pH 4.5, 2 M sodium formate, 4 mM PLP_Snyder608

Crystal Properties
Matthews coefficient	Solvent content
3.85	68.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.075	α = 90
b = 85.075	β = 90
c = 132.548	γ = 120

Symmetry
Space Group	P 32 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 PILATUS3 X 6M		2020-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9792	APS	19-ID

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	1.79	42.57	100	0.111	0.117	0.035	0.995	6.9	10.8		52971

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	1.79	1.82	99.7		1.69	1.805	0.626	0.534	1.07	8.1

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	6WRH	1.79	42.57	50314	2615	99.5	0.1681	0.1671	0.17	0.1877	0.19	RANDOM	45.221

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]
0.13	0.07		0.13		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.948
r_dihedral_angle_4_deg	17.779
r_dihedral_angle_3_deg	14.603
r_dihedral_angle_1_deg	6.08
r_angle_refined_deg	1.584
r_angle_other_deg	1.511
r_chiral_restr	0.074
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.948
r_dihedral_angle_4_deg	17.779
r_dihedral_angle_3_deg	14.603
r_dihedral_angle_1_deg	6.08
r_angle_refined_deg	1.584
r_angle_other_deg	1.511
r_chiral_restr	0.074
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.008
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2486
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	32

Software

Software
Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	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.