9HC1 | pdb_00009hc1

SARS-CoV-2 Main Protease complexed with (1R)-N-(3-chlorophenyl)-3-oxo-N-[4-(2-oxopyrrolidin-1-yl)phenyl]indane-1-carboxamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7NTT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	0.2M NaFORMATE pH7.5, 20% PEG 3350 then soaking with inhibitor (DMSO) and cryo-protected with 10% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.879	α = 114.926
b = 53.72	β = 100.263
c = 63.589	γ = 90.02

Symmetry
Space Group	P 1

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 9M		2022-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.980117	SOLEIL	PROXIMA 2

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	1.49	48.589	94.4	0.167	0.236	0.167	0.972	6.8	3.6		81151			14.66

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	1.49	1.52			0.936	5.913	4.181	0.101		2.8

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	1.493	48.589	81149	4023	94.537	0.183	0.1813	0.1901	0.2199	0.2239	17.029

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]
-0.381	0.202	-0.039	-1.071	0.238	0.812

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.09
r_dihedral_angle_3_deg	14.879
r_dihedral_angle_2_deg	12.168
r_dihedral_angle_1_deg	7.433
r_angle_refined_deg	2.036
r_angle_other_deg	0.689
r_symmetry_nbd_refined	0.297
r_symmetry_xyhbond_nbd_refined	0.242
r_nbd_other	0.24
r_nbd_refined	0.22
r_xyhbond_nbd_refined	0.199
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.185
r_chiral_restr	0.109
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.015
r_gen_planes_refined	0.014
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4712
Nucleic Acid Atoms
Solvent Atoms	571
Heterogen Atoms	85

Software

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