Experiment: 7YDF

Crystal structure of human SARS2 catalytic domain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WLE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	Na citrate, PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.85	α = 90
b = 89.85	β = 90
c = 86.22	γ = 120

Symmetry
Space Group	P 31 1 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 6M		2021-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97853	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.8	44.92	97.6	0.17	0.18	0.059	0.997	8.3	9.6		18615			84.81

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	2.8	2.95	100		2.572	2.713	0.859	0.354		9.9

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	THROUGHOUT	1WLE	2.8	44.92	0.02	18615	872	96.97	0.2905	0.2886	0.2883	0.3325	0.3281	98.5092

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1988
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing