9GF7 | pdb_00009gf7

SARS-CoV2 Main Protease (Mpro) in complex with the covalent inhibitor 28a

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Y2E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		290.15	22-27% PEG1500, 100mM MTT buffer [DL-Malic acid, 4-Morpholine Ethane Sulfonic acid (MES) monohydrate, 2-Amino-2- (hydroxymethyl)-1,3- propanediol (TRIS)-HCl), pH=6.0].

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.914	α = 90
b = 53.134	β = 101.158
c = 114.429	γ = 90

Symmetry
Space Group	I 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 EIGER2 X 9M		2022-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8731	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.9	48.073	99.32	0.084	0.995	7.6	3.6		20880

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.968			0.9	0.299

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.9	48.073	20879	1078	99.348	0.258	0.2563	0.2593	0.2931	0.2922	34.213

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]
-0.113		0.721	0.231		-0.373

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.51
r_dihedral_angle_other_2_deg	14.435
r_dihedral_angle_3_deg	12.587
r_dihedral_angle_6_deg	12.389
r_dihedral_angle_1_deg	6.565
r_lrange_it	4.022
r_lrange_other	3.991
r_scangle_it	1.974
r_scangle_other	1.974
r_mcangle_other	1.814
r_mcangle_it	1.813
r_angle_refined_deg	1.232
r_scbond_it	1.203
r_scbond_other	1.202
r_angle_other_deg	1.164
r_mcbond_it	1.129
r_mcbond_other	1.125
r_symmetry_nbd_other	0.217
r_nbd_other	0.215
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.202
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.111
r_symmetry_nbd_refined	0.102
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.064
r_symmetry_xyhbond_nbd_other	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.009
r_bond_refined_d	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2398
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing