7KOK | pdb_00007kok

The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder496 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, HANGING DROP	6	277	0.1 M MES buffer, 0.2 M zinc acetate, 10% PEG 8000, 4 mM PLP_Snyder496

Crystal Properties
Matthews coefficient	Solvent content
4.93	75.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.554	α = 90
b = 113.554	β = 90
c = 219.682	γ = 90

Symmetry
Space Group	I 41 2 2

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		2020-06-29	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	2	41.76	99.9	0.138	0.141	0.03	0.996	6.3	20.6		48260

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	2.03	99.1		1.719	1.784	0.46	0.6		14

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	2	41.76	45790	2443	99.63	0.1854	0.184	0.19	0.2106	0.22	RANDOM	61.067

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]
2			2		-4.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.042
r_dihedral_angle_4_deg	23.418
r_dihedral_angle_3_deg	16.28
r_dihedral_angle_1_deg	6.874
r_angle_refined_deg	1.588
r_angle_other_deg	1.311
r_chiral_restr	0.067
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.042
r_dihedral_angle_4_deg	23.418
r_dihedral_angle_3_deg	16.28
r_dihedral_angle_1_deg	6.874
r_angle_refined_deg	1.588
r_angle_other_deg	1.311
r_chiral_restr	0.067
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2483
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	64

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.