7NTW

Crystal structure of the SARS-CoV-2 Main Protease with a Zinc ion coordinated in the active site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7K3T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2M NaFormate, 20% PEG 3350, 10% DMSO, 10% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.31	α = 90
b = 53.68	β = 101.67
c = 44.72	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 EIGER X 16M		2020-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.978564	SOLEIL	PROXIMA 1

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	1.815	48.37	99	0.998	12.8	6.9		23721

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	1.815	1.85	94.2		0.423

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	7K3T	1.815	48.37	23721	1186	99.114	0.2	0.1966	0.257	38.006

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]
1.697		0.097	0.197		-1.782

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.47
r_dihedral_angle_4_deg	14.837
r_dihedral_angle_3_deg	13.21
r_dihedral_angle_1_deg	7.882
r_lrange_it	6.784
r_lrange_other	6.729
r_scangle_it	4.779
r_scangle_other	4.779
r_mcangle_it	3.841
r_mcangle_other	3.84
r_scbond_it	3.274
r_scbond_other	3.268
r_mcbond_it	2.836
r_mcbond_other	2.835
r_angle_refined_deg	1.461
r_angle_other_deg	1.305
r_symmetry_xyhbond_nbd_refined	0.225
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.21
r_nbd_other	0.2
r_symmetry_nbd_other	0.188
r_symmetry_nbd_refined	0.18
r_nbtor_refined	0.166
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.063
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2351
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data reduction
Aimless	data scaling
MOLREP	phasing
XDS	data processing
Coot	model building