8E26

Crystal Structure of SARS-CoV-2 Main Protease N142S 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	7MBG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		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	52.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.841	α = 90
b = 100.619	β = 90
c = 103.356	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS PILATUS 2M		2022-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS SIRUS BEAMLINE MANACA	0.9772	LNLS SIRUS	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	1.845	56.313	39.62	0.949	4.4	4		24397

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	1.845	2.207	10.2		0.823	1.5

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	1.845	56.313	24393	1192	39.632	0.226	0.2242	0.2654	17.926

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]
0.536			0.203		-0.738

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.53
r_dihedral_angle_4_deg	18.586
r_dihedral_angle_3_deg	16.447
r_dihedral_angle_1_deg	7.152
r_lrange_it	4.11
r_lrange_other	4.059
r_mcangle_other	2.077
r_mcangle_it	2.075
r_scangle_it	1.892
r_scangle_other	1.892
r_angle_refined_deg	1.289
r_angle_other_deg	1.268
r_mcbond_it	1.172
r_mcbond_other	1.161
r_scbond_it	1.065
r_scbond_other	1.064
r_symmetry_xyhbond_nbd_refined	0.381
r_nbd_other	0.228
r_xyhbond_nbd_refined	0.226
r_symmetry_nbd_refined	0.218
r_symmetry_nbd_other	0.201
r_nbd_refined	0.192
r_nbtor_refined	0.162
r_symmetry_xyhbond_nbd_other	0.157
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.054
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4732
Nucleic Acid Atoms
Solvent Atoms	219
Heterogen Atoms	78

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing