8G62

Papain-Like Protease of SARS CoV-2 in complex with remodilin NCGC 390004

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	7	277	0.1 M Bis_tris propane, pH 7.0, 2.8 M sodium acetate, 0.1 M glycine, 4 mM ligand

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 170.02	α = 90
b = 170.02	β = 90
c = 97.588	γ = 90

Symmetry
Space Group	P 41 21 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		2021-01-29	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)	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	2.17	49.06	100	0.143	1	7.1	12.7		75825

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.17	2.21	100		1.979	0.507	1.27	11.9

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.17	49.06	71961	3793	99.93	0.18134	0.17962	0.21445	RANDOM	55.623

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]
-0.08			-0.08		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.836
r_dihedral_angle_4_deg	17.673
r_dihedral_angle_3_deg	15.231
r_dihedral_angle_1_deg	6.267
r_long_range_B_refined	6.116
r_long_range_B_other	6.105
r_scangle_other	4.196
r_mcangle_it	2.878
r_mcangle_other	2.878
r_scbond_it	2.648
r_scbond_other	2.648
r_mcbond_it	1.957
r_mcbond_other	1.955
r_angle_refined_deg	1.61
r_angle_other_deg	1.274
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7463
Nucleic Acid Atoms
Solvent Atoms	264
Heterogen Atoms	227

Software

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