8EYJ

Crystal Structure of uncleaved SARS-CoV-2 Main Protease C145S 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		293	0.1 M MES pH 6.7, 5% DMSO, 8% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.646	α = 90
b = 101.969	β = 90
c = 103.626	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	100	PIXEL	DECTRIS PILATUS 2M		2022-05-19	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)	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	1.738	101.969	71.5	0.07	0.995	8.9	6.7		53189

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.738	1.8			0.476	0.556	1.4

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	1.738	72.788	53188	2594	71.5	0.195	0.1931	0.2339	25.399

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]
-0.009			0.172		-0.163

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.243
r_dihedral_angle_4_deg	17.571
r_dihedral_angle_3_deg	13.138
r_lrange_it	7.473
r_dihedral_angle_1_deg	7.29
r_lrange_other	7.071
r_scangle_it	4.13
r_scangle_other	4.129
r_mcangle_other	3.367
r_mcangle_it	3.366
r_scbond_it	2.603
r_scbond_other	2.603
r_mcbond_other	2.11
r_mcbond_it	2.109
r_angle_refined_deg	1.487
r_angle_other_deg	1.423
r_symmetry_xyhbond_nbd_refined	0.285
r_xyhbond_nbd_refined	0.228
r_nbd_other	0.216
r_nbd_refined	0.204
r_symmetry_nbd_other	0.199
r_symmetry_nbd_refined	0.197
r_nbtor_refined	0.169
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.075
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4684
Nucleic Acid Atoms
Solvent Atoms	713
Heterogen Atoms	70

Software

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