7NTT

Crystal structure of the SARS-CoV-2 Main Protease

X-RAY DIFFRACTION

---

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
2	38.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.76	α = 90
b = 53.98	β = 101.18
c = 114.35	γ = 90

Symmetry
Space Group	P 1 21 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	1.743	48.64	95	0.993	7.72	6.2		52176

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	1.743	1.85	69.2		0.509

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	1.743	43.949	52172	2609	95.01	0.21	0.2073	0.2547	29.063

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]
0.126		-1.221	0.311		0.042

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.565
r_dihedral_angle_4_deg	20.42
r_dihedral_angle_3_deg	14.528
r_dihedral_angle_1_deg	7.834
r_lrange_other	6.356
r_lrange_it	6.354
r_scangle_it	4.362
r_scangle_other	4.362
r_mcangle_it	3.406
r_mcangle_other	3.406
r_scbond_it	2.782
r_scbond_other	2.781
r_mcbond_it	2.277
r_mcbond_other	2.277
r_angle_refined_deg	1.538
r_angle_other_deg	1.353
r_symmetry_xyhbond_nbd_refined	0.207
r_nbd_refined	0.195
r_xyhbond_nbd_refined	0.188
r_symmetry_nbd_other	0.179
r_xyhbond_nbd_other	0.179
r_symmetry_nbd_refined	0.173
r_nbd_other	0.172
r_nbtor_refined	0.167
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4727
Nucleic Acid Atoms
Solvent Atoms	277
Heterogen Atoms	7

Software

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