8EHJ | pdb_00008ehj

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) H172Q Mutant

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	25% PEG 3350, 0.1M Potassium/Sodium Tartrate, 0.005M Magnesium Chloride

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.865	α = 90
b = 53.461	β = 101.31
c = 113.543	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 PILATUS3 6M		2022-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.0	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.28	50	98.3	0.112	21.23	6.3		23984

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.28	2.32			0.472	2.21

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7LYH	2.28	48.24	22787	1186	98.7	0.2163	0.2144	0.22	0.2501	0.26	RANDOM	54.871

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]
-2.14		0.31	-1.52		3.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.7
r_dihedral_angle_3_deg	12.668
r_dihedral_angle_4_deg	11.115
r_dihedral_angle_1_deg	5.783
r_angle_refined_deg	1.066
r_angle_other_deg	1.038
r_chiral_restr	0.087
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4703
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing