8DZ6

Crystal Structure of SARS-CoV-2 Main protease mutant Q189K 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
2.63	53.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.782	α = 90
b = 101.572	β = 90
c = 103.561	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 SIRUS BEAMLINE MANACA	0.977180	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	2.366	72.52	56.9	0.997	4.6	5.3		16996

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	2.366	2.45			0.683

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	2.366	72.515	16996	1700	56.906	0.235	0.2286	0.2961	31.972

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]
-0.194			0.236		-0.042

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.56
r_dihedral_angle_4_deg	25.075
r_dihedral_angle_3_deg	16.796
r_dihedral_angle_1_deg	7.801
r_lrange_other	4.714
r_lrange_it	4.698
r_scangle_it	2.715
r_scangle_other	2.714
r_mcangle_it	2.701
r_mcangle_other	2.701
r_scbond_it	1.588
r_scbond_other	1.588
r_mcbond_it	1.578
r_mcbond_other	1.577
r_angle_refined_deg	1.388
r_angle_other_deg	1.316
r_symmetry_xyhbond_nbd_refined	0.486
r_nbd_other	0.379
r_symmetry_nbd_refined	0.372
r_symmetry_xyhbond_nbd_other	0.245
r_nbd_refined	0.211
r_symmetry_nbd_other	0.21
r_xyhbond_nbd_other	0.208
r_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.169
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.056
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4687
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	82

Software

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