8E25 | pdb_00008e25

Crystal Structure of SARS-CoV-2 Main Protease M49I 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% DMSO, 8% PEG 4000 Cryo protected with 40% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.859	α = 90
b = 100.068	β = 90
c = 103.533	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)	Rpim I (All)	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	1.868	72.056	51.42	0.084	0.989	7.4	5.6		30317

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	1.868	1.937	2.37		0.377	0.684	1.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7MBG	1.868	72.056	30317	1493	51.246	0.196	0.194	0.2	0.24	0.25	33.494

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]
0.206			0.119		-0.325

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.833
r_dihedral_angle_3_deg	16.561
r_dihedral_angle_4_deg	16.488
r_dihedral_angle_1_deg	7.838
r_lrange_it	6.779
r_lrange_other	6.749
r_scangle_it	4.348
r_scangle_other	4.348
r_mcangle_it	3.735
r_mcangle_other	3.734
r_scbond_it	2.66
r_scbond_other	2.66
r_mcbond_it	2.289
r_mcbond_other	2.288
r_angle_refined_deg	1.454
r_angle_other_deg	1.274
r_symmetry_xyhbond_nbd_refined	0.28
r_nbd_other	0.234
r_xyhbond_nbd_refined	0.214
r_nbd_refined	0.193
r_symmetry_nbd_other	0.192
r_symmetry_nbd_refined	0.168
r_nbtor_refined	0.164
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.062
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	4680
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	82

Software

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