9H4B | pdb_00009h4b

Crystal structure of SARS-CoV-2 Mpro in complex with GK-730

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	7.5	294	0.02M Sodium potassium phosphate pH7.5, 20% w/v PEG 3350, 10% v/v Ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.777	α = 90
b = 52.896	β = 98.94
c = 45.648	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		2024-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

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	1.9	48.01	98.96	0.998	9.19	13.8		21422

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	1.9	1.968			0.556

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	48.01	21420	1066	98.979	0.175	0.1723	0.1847	0.2309	0.2413	30.805

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]
1.594		-1.996	-1.038		0.068

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.939
r_dihedral_angle_3_deg	15.39
r_dihedral_angle_2_deg	15.065
r_lrange_it	7.839
r_lrange_other	7.824
r_dihedral_angle_1_deg	7.312
r_scangle_it	6.262
r_scangle_other	6.261
r_scbond_it	4.083
r_scbond_other	4.082
r_mcangle_it	3.626
r_mcangle_other	3.626
r_dihedral_angle_other_3_deg	2.912
r_mcbond_it	2.755
r_mcbond_other	2.732
r_dihedral_angle_other_2_deg	2.42
r_angle_refined_deg	1.592
r_angle_other_deg	0.542
r_nbd_refined	0.217
r_symmetry_nbd_other	0.201
r_nbd_other	0.199
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.156
r_symmetry_nbd_refined	0.145
r_symmetry_xyhbond_nbd_refined	0.116
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.077
r_bond_refined_d	0.008
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	2367
Nucleic Acid Atoms
Solvent Atoms	139
Heterogen Atoms	45

Software

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