7NFV

Structure of SARS-CoV-2 Papain-like protease PLpro

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7JRN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277	1.0M NaH2PO4/1.0MKH2PO4 100mM Tris_HCl pH=7.5

Crystal Properties
Matthews coefficient	Solvent content
3.68	66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.33	α = 90
b = 82.33	β = 90
c = 134.32	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 PILATUS 6M		2020-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.42	48.89	100	0.97	28.3	52.9		99793

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.42	1.44			0.36

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7jrn	1.42	48.89	99791	4919	99.989	0.155	0.1538	0.1714	31.543

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]
0.299	0.15		0.299		-0.972

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.599
r_dihedral_angle_3_deg	14.271
r_dihedral_angle_4_deg	12.021
r_lrange_it	7.261
r_lrange_other	6.907
r_dihedral_angle_1_deg	6.089
r_scangle_it	5.636
r_scangle_other	5.631
r_scbond_it	3.892
r_scbond_other	3.89
r_mcangle_it	2.607
r_mcangle_other	2.606
r_angle_refined_deg	2.308
r_mcbond_it	1.94
r_mcbond_other	1.939
r_angle_other_deg	1.609
r_symmetry_nbd_refined	0.314
r_symmetry_xyhbond_nbd_refined	0.266
r_xyhbond_nbd_refined	0.245
r_nbd_refined	0.244
r_nbd_other	0.213
r_nbtor_refined	0.187
r_symmetry_nbd_other	0.18
r_chiral_restr	0.119
r_symmetry_xyhbond_nbd_other	0.091
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.02
r_gen_planes_refined	0.014
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2502
Nucleic Acid Atoms
Solvent Atoms	530
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing