8DZ2

Crystal Structure of SARS-CoV-2 Main protease 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
2.48	50.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.319	α = 90
b = 97.536	β = 90
c = 102.327	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	2.129	70.701	98.6	0.99	8.6	5.1		37960

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	2.129	2.206			0.763	2.3

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	2.129	70.701	37959	1898	98.633	0.191	0.1891	0.2295	34.824

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]
-1.906			2.956		-1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.991
r_dihedral_angle_4_deg	20.551
r_dihedral_angle_3_deg	14.788
r_dihedral_angle_1_deg	7.935
r_lrange_it	6.677
r_lrange_other	6.652
r_scangle_it	4.976
r_scangle_other	4.976
r_mcangle_other	3.808
r_mcangle_it	3.807
r_scbond_it	3.28
r_scbond_other	3.279
r_mcbond_it	2.585
r_mcbond_other	2.583
r_angle_refined_deg	1.55
r_angle_other_deg	1.392
r_nbd_refined	0.203
r_symmetry_nbd_other	0.201
r_symmetry_xyhbond_nbd_other	0.2
r_xyhbond_nbd_refined	0.196
r_nbd_other	0.191
r_symmetry_xyhbond_nbd_refined	0.172
r_nbtor_refined	0.17
r_symmetry_nbd_refined	0.158
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.069
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
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	259
Heterogen Atoms	82

Software

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