8CAE | pdb_00008cae

Crystal structure of SARS-CoV-2 Mpro-H172Y mutant in complex with nirmatrelvir

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Y2G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	0.1M MMT pH8.0, 25% w/vPEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2	38.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.208	α = 90
b = 53.761	β = 101.585
c = 45.551	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		2022-10-22	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)	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	2.65	48.583	98.7	0.986	6	3.9		7973

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	2.72	2.86			0.327

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	NONE	2.65	48.583	7973	398	98.884	0.181	0.1765	0.184	0.258	0.2607	79.122

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]
4.402		3.017	-2.435		-2.956

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.096
r_dihedral_angle_3_deg	15.818
r_lrange_it	14.585
r_lrange_other	14.583
r_dihedral_angle_6_deg	14.253
r_dihedral_angle_other_3_deg	12.615
r_scangle_it	10.236
r_scangle_other	10.234
r_mcangle_it	9.619
r_mcangle_other	9.616
r_dihedral_angle_1_deg	8.745
r_scbond_it	6.423
r_scbond_other	6.42
r_mcbond_it	6.298
r_mcbond_other	6.286
r_angle_refined_deg	1.373
r_angle_other_deg	0.49
r_nbd_refined	0.242
r_symmetry_nbd_other	0.214
r_nbd_other	0.211
r_nbtor_refined	0.193
r_xyhbond_nbd_refined	0.191
r_symmetry_xyhbond_nbd_refined	0.167
r_symmetry_nbd_refined	0.157
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.085
r_chiral_restr	0.066
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2342
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	35

Software

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