6XA4 | pdb_00006xa4

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with UAW241

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YB7	PDB entry 6YB7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	20% PEG3000, 0.1 M sodium citrate, pH 5.6

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.538	α = 90
b = 54.204	β = 100.71
c = 45.414	γ = 90

Symmetry
Space Group	C 1 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		2020-05-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.978	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.65	50	98.2	0.065	0.075	0.036	8.2	4.1		32214

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	1.65	1.68	94.1		0.633	0.748	0.389	0.675		3.3

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	PDB entry 6YB7	1.65	38.54	30615	1599	97.91	0.2002	0.1982	0.2058	0.2393	0.2477	RANDOM	30.825

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]
1.9		-1.05	-0.24		-1.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.896
r_dihedral_angle_4_deg	22.873
r_dihedral_angle_3_deg	14.557
r_dihedral_angle_1_deg	7.653
r_angle_refined_deg	1.631
r_angle_other_deg	1.393
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2343
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	33

Software

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