7JIW | pdb_00007jiw

The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder530 inhibitor

X-RAY DIFFRACTION

Starting Model(s)

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

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_Snyder530

Crystal Properties
Matthews coefficient	Solvent content
4.95	75.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.648	α = 90
b = 113.648	β = 90
c = 220.574	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)	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	2.3	45.51	99.9	0.095	0.097	0.021	6.3	20.9		32308			66.3

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	2.3	2.34	99		1.731	1.788	0.428	0.605	0.97	14.6

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	6WZU	2.3	45.51	30715	1564	99.85	0.2135	0.2121	0.21	0.2395	0.24	RANDOM	82.634

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]
2.87			2.87		-5.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.544
r_dihedral_angle_3_deg	15.408
r_dihedral_angle_4_deg	14.762
r_dihedral_angle_1_deg	6.843
r_angle_refined_deg	1.489
r_angle_other_deg	1.214
r_chiral_restr	0.059
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_gen_planes_other	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.544
r_dihedral_angle_3_deg	15.408
r_dihedral_angle_4_deg	14.762
r_dihedral_angle_1_deg	6.843
r_angle_refined_deg	1.489
r_angle_other_deg	1.214
r_chiral_restr	0.059
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_gen_planes_other	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2422
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
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.