8DZA

Crystal Structure of SARS-CoV-2 Main protease A193T 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% v/v DMSO, 8% w/v PEG4000, 30% w/v PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.989	α = 90
b = 99.979	β = 90
c = 103.638	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		2022-04-27	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	1.96	72.06	58.7	0.991	7.8	7.8		29962

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	1.96	2.03			0.253

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	1.961	72.058	29962	1458	58.32	0.203	0.2007	0.2419	34.182

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]
0.012			0.189		-0.201

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.765
r_dihedral_angle_4_deg	19.574
r_dihedral_angle_3_deg	15.479
r_lrange_it	7.912
r_lrange_other	7.905
r_dihedral_angle_1_deg	7.68
r_scangle_it	4.428
r_scangle_other	4.428
r_mcangle_it	3.458
r_mcangle_other	3.458
r_scbond_it	2.81
r_scbond_other	2.81
r_mcbond_it	2.15
r_mcbond_other	2.147
r_angle_refined_deg	1.417
r_angle_other_deg	1.282
r_nbd_other	0.339
r_symmetry_xyhbond_nbd_refined	0.32
r_symmetry_xyhbond_nbd_other	0.318
r_symmetry_nbd_refined	0.277
r_xyhbond_nbd_refined	0.22
r_nbd_refined	0.206
r_symmetry_nbd_other	0.202
r_nbtor_refined	0.165
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.061
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4691
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	90

Software

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