8CA6 | pdb_00008ca6

Crystal structure of SARS-CoV-2 Mpro-Q189K mutant, free enzyme

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other	6y2e

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.2M Sodium formate, 0.1M Bis-Tris propane pH6.5, 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.75	α = 90
b = 106.633	β = 104.725
c = 53.589	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		2022-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033	PETRA III, DESY	P11

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	1.92	46.61	98.4	0.065	0.998	8.5	3.5		40519

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	1.92	1.97			0.587

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	1.92	46.61	40494	1966	98.277	0.239	0.2361	0.25	0.2944	0.31	47.455

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]
5.191		-1.458	-3.797		-0.552

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.707
r_dihedral_angle_3_deg	18.549
r_dihedral_angle_4_deg	18.003
r_lrange_it	9.198
r_lrange_other	9.198
r_dihedral_angle_1_deg	8.31
r_scangle_it	6.276
r_scangle_other	6.275
r_mcangle_it	6.001
r_mcangle_other	6
r_scbond_it	4.142
r_scbond_other	4.141
r_mcbond_it	4.138
r_mcbond_other	4.138
r_angle_refined_deg	1.594
r_angle_other_deg	1.254
r_nbd_other	0.24
r_nbd_refined	0.221
r_symmetry_nbd_refined	0.216
r_symmetry_nbd_other	0.197
r_xyhbond_nbd_refined	0.179
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.129
r_symmetry_xyhbond_nbd_other	0.115
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.065
r_bond_refined_d	0.008
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	4696
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms

Software

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