8C9P | pdb_00008c9p

Crystal structure of SARS-CoV-2 Mpro-E166V mutant, free enzyme

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		298	0.1MBis Tris Propane pH 6.50.2 MPotassium thiocyanate20 % w/vPEG 335010% v/vEthylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2	38.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.594	α = 90
b = 53.93	β = 101.003
c = 44.754	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 PILATUS 6M-F		2022-08-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.003	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	2	48.55	98.77	0.999	13.62	5		17883			41.61

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	2	2.072	98.77		0.9355	0.577

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	2	48.55	17883	872	98.779	0.216	0.2126	0.22	0.277	0.28	48.789

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]
2.636		0.088	-0.462		-2.053

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.271
r_dihedral_angle_4_deg	18.325
r_dihedral_angle_3_deg	17.666
r_lrange_it	8.638
r_lrange_other	8.638
r_dihedral_angle_1_deg	8.335
r_scangle_it	6.757
r_scangle_other	6.756
r_mcangle_it	5.923
r_mcangle_other	5.921
r_scbond_it	4.905
r_scbond_other	4.903
r_mcbond_it	4.507
r_mcbond_other	4.497
r_angle_refined_deg	1.613
r_angle_other_deg	1.349
r_nbd_refined	0.221
r_nbd_other	0.201
r_symmetry_nbd_refined	0.195
r_symmetry_nbd_other	0.193
r_xyhbond_nbd_refined	0.183
r_nbtor_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.143
r_symmetry_xyhbond_nbd_other	0.089
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.071
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	2356
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms

Software

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