9HBQ | pdb_00009hbq

SARS-CoV-2 Main Protease complexed with (1R)-N-(3-chlorophenyl)-3-oxo-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	7K3T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	0.2M NaFORMATE, 20% PEG 3350 then soaking with inhibitor (in DSMO) and cryoprotected with 10% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2	38.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.95	α = 90
b = 53.6	β = 100.94
c = 44.62	γ = 90

Symmetry
Space Group	C 1 2 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		2022-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.91840	SOLEIL	PROXIMA 2

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	1.795	48.464	99.4	0.069	0.999	25.02	6.7		24927			19.85

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.795	1.9			0.276	0.98	7.81

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	1.795	48.464	24927	1247	99.497	0.161	0.1579	0.1575	0.2109	0.2101	19.789

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]
1.328		0.018	-0.194		-1.062

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.226
r_dihedral_angle_2_deg	14.327
r_dihedral_angle_3_deg	13.966
r_dihedral_angle_1_deg	7.18
r_lrange_it	5.624
r_lrange_other	5.515
r_scangle_it	4.13
r_scangle_other	4.129
r_scbond_it	2.805
r_scbond_other	2.804
r_mcangle_it	2.531
r_mcangle_other	2.53
r_mcbond_it	1.833
r_mcbond_other	1.825
r_angle_refined_deg	1.538
r_angle_other_deg	0.516
r_nbd_refined	0.222
r_symmetry_xyhbond_nbd_refined	0.208
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.179
r_symmetry_nbd_refined	0.16
r_nbd_other	0.149
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.075
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2347
Nucleic Acid Atoms
Solvent Atoms	267
Heterogen Atoms	34

Software

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