8DZ9

Crystal Structure of SARS-CoV-2 Main protease G143S mutant in complex with Nirmatrelvir

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.1 M MES, pH 6.7, 5% v/v DMSO, 8% w/v PEG4000, 30% w/v PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.686	α = 90
b = 102.808	β = 91.289
c = 101.554	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 PILATUS 2M		2022-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS SIRIUS BEAMLINE MANACA	0.977180	LNLS SIRIUS	MANACA

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	1.66	101.53	46.1	0.968	3.7	3.2		74929

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	1.66	1.72			0.463

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7mbg	1.664	101.528	74928	3690	46.108	0.21	0.2077	0.2506	19.413

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]
-1.973		-0.318	-3.408		5.381

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.36
r_dihedral_angle_4_deg	18.383
r_dihedral_angle_3_deg	16.949
r_dihedral_angle_1_deg	8.792
r_lrange_it	6.285
r_lrange_other	6.061
r_mcangle_it	2.264
r_mcangle_other	2.264
r_scangle_it	2.225
r_scangle_other	2.225
r_angle_refined_deg	1.973
r_mcbond_it	1.484
r_mcbond_other	1.484
r_scbond_it	1.475
r_scbond_other	1.475
r_angle_other_deg	1.254
r_xyhbond_nbd_refined	0.415
r_symmetry_xyhbond_nbd_refined	0.395
r_symmetry_nbd_refined	0.265
r_nbd_other	0.235
r_nbd_refined	0.218
r_symmetry_nbd_other	0.208
r_symmetry_xyhbond_nbd_other	0.191
r_nbtor_refined	0.165
r_xyhbond_nbd_other	0.149
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9356
Nucleic Acid Atoms
Solvent Atoms	639
Heterogen Atoms	144

Software

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