7M1Y | pdb_00007m1y

The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with ebselen

X-RAY DIFFRACTION

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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	8.5	277	0.1 M Tris-Cl, pH 8.5, 3.5 M sodium formate, 0.1 M sodium iodide, 4 mM ebselen

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.887	α = 90
b = 114.887	β = 90
c = 252.82	γ = 120

Symmetry
Space Group	P 65 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 6M		2020-12-16	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	2.02	49.8	100	0.15	0.154	0.035	1	5	18.7		65358

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	2.02	2.05	100		3.052	3.153	0.785	0.553	0.96	15.6

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	6WRH	2.02	49.8	61978	3276	99.92	0.1856	0.1841	0.1909	0.2129	0.2175	RANDOM	56.594

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]
0.95	0.48		0.95		-3.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.252
r_dihedral_angle_3_deg	16.365
r_dihedral_angle_4_deg	15.058
r_dihedral_angle_1_deg	6.219
r_angle_refined_deg	1.614
r_angle_other_deg	1.332
r_chiral_restr	0.07
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4969
Nucleic Acid Atoms
Solvent Atoms	234
Heterogen Atoms	75

Software

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