8B2T

SARS-CoV-2 Main Protease (Mpro) in complex with nirmatrelvir alkyne

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YB7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	11% (v/v) PEG 4K, 5% (v/v) DMSO, 0.1 M MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.037	α = 90
b = 64.392	β = 90
c = 104.952	γ = 90

Symmetry
Space Group	P 21 21 2

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 PILATUS3 X CdTe 2M		2022-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE VMXm	0.58124	Diamond	VMXm

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.89	22.48	79.1	0.543	0.569	0.162	0.984	7.6	16.4		20055

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.89	1.94			7.222	7.519	2.055	0.475		22.4

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	6yb7	1.893	22.48	19991	995	78.029	0.184	0.1824	0.2234	30.792

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]
-0.679			0.232		0.447

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.537
r_dihedral_angle_3_deg	13.417
r_lrange_other	10.184
r_lrange_it	10.18
r_scangle_it	8.633
r_scangle_other	8.631
r_dihedral_angle_2_deg	7.264
r_dihedral_angle_1_deg	7.236
r_scbond_it	6.502
r_scbond_other	6.499
r_mcangle_other	6.301
r_mcangle_it	6.291
r_mcbond_it	4.633
r_mcbond_other	4.62
r_angle_refined_deg	1.419
r_angle_other_deg	0.472
r_nbd_refined	0.206
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.142
r_symmetry_xyhbond_nbd_refined	0.122
r_nbd_other	0.114
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.069
r_symmetry_nbd_refined	0.067
r_dihedral_angle_other_1_deg	0.007
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2359
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB-REDO	refinement
Aimless	data scaling
xia2.multiplex	data scaling
MOLREP	phasing
xia2.multiplex	data reduction