Experiment: 8FWN

Crystal structure of SARS-CoV-2 papain-like protease C111S mutant

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	100 mM Sodium acetate, 0.8 M Monosodium phosphate, 1.2 M Dipotassium hydrogen phosphate

Crystal Properties
Matthews coefficient	Solvent content
3.54	65.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.8	α = 90
b = 82.8	β = 90
c = 134.396	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 2M		2021-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS SIRUS BEAMLINE MANACA	0.977	LNLS SIRUS	MANACA

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	1.5	44.8	99.99	0.999	17.26	2		85860			20.72

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	1.5	1.554			0.522

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7CMD	1.5	44.8	1.34	85855	4291	99.99	0.1825	0.1816	0.1848	0.1983	0.2013	26.06

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.5388
f_angle_d	1.3893
f_chiral_restr	0.086
f_bond_d	0.0157
f_plane_restr	0.0095

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2468
Nucleic Acid Atoms
Solvent Atoms	461
Heterogen Atoms	45

Software

Software
Software Name	Purpose
autoPROC	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement