8C9U | pdb_00008c9u

Crystal structure of SARS-CoV-2 Mpro-Q189K mutant in complex with nirmatrelvir

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other	6y2e

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.2M Sodium citrate tribasic dihydrate, 20% w/vPEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.213	α = 90
b = 64.476	β = 90
c = 105.301	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 EIGER X 16M		2022-08-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.75	41.58	100	0.154	0.997	9.5	9.6		31773

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	1.75	1.78			0.621

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.75	41.58	31745	1544	99.711	0.189	0.1876	0.1971	0.2101	0.2156	21.676

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]
-1.106			0.816		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.679
r_dihedral_angle_4_deg	16.683
r_dihedral_angle_3_deg	15.248
r_dihedral_angle_1_deg	7.6
r_lrange_it	5.9
r_lrange_other	5.859
r_scangle_it	4.448
r_scangle_other	4.447
r_scbond_it	2.96
r_scbond_other	2.959
r_mcangle_other	2.838
r_mcangle_it	2.836
r_mcbond_it	1.967
r_mcbond_other	1.943
r_angle_refined_deg	1.688
r_dihedral_angle_other_3_deg	1.586
r_angle_other_deg	1.474
r_symmetry_nbd_refined	0.32
r_nbd_refined	0.208
r_nbd_other	0.199
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.163
r_xyhbond_nbd_refined	0.157
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2358
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	35

Software

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