8X1X | pdb_00008x1x

SARS-CoV-2 Papain like protease (PLpro) in complex with inhibitor Lithocholic acid

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, SITTING DROP		277.15	0.1 M Tris-HCl (pH 7.5-9.0), 1.4 M NaH2PO4, 2-15% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.590202	65.76138

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.732	α = 90
b = 81.732	β = 90
c = 133.689	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	RIGAKU HyPix-6000HE		2023-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	24.84	99.9	0.172	0.913	2.5	4		23592

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38	99.9		0.576	0.381	0.616		5.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.3	24.838	23561	1207	99.86	0.241	0.2386	0.2259	0.2844	0.2655	37.53

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]
-0.49			-0.49		0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.578
r_dihedral_angle_6_deg	12.957
r_lrange_it	10.275
r_dihedral_angle_1_deg	8.772
r_dihedral_angle_2_deg	8.294
r_scangle_it	6.185
r_mcangle_it	5.906
r_scbond_it	4.518
r_mcbond_it	4.242
r_angle_refined_deg	2.535

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.578
r_dihedral_angle_6_deg	12.957
r_lrange_it	10.275
r_dihedral_angle_1_deg	8.772
r_dihedral_angle_2_deg	8.294
r_scangle_it	6.185
r_mcangle_it	5.906
r_scbond_it	4.518
r_mcbond_it	4.242
r_angle_refined_deg	2.535
r_symmetry_nbd_refined	0.418
r_nbtor_refined	0.334
r_nbd_refined	0.276
r_symmetry_xyhbond_nbd_refined	0.257
r_xyhbond_nbd_refined	0.241
r_chiral_restr	0.208
r_gen_planes_refined	0.009
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2501
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	100

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
MOLREP	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.