9HJH | pdb_00009hjh

Structure of compound 1 bound to SARS-CoV-2 main protease

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		internal structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	25% PEG 3350, 0.1M HEPES pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.799	α = 90
b = 101.274	β = 90
c = 104.099	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 EIGER2 XE CdTe 16M		2024-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.89	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.197	56.9	99.9	0.1	0.05	0.996	11.3	9.9		223287

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.197	1.218			0.728	0.367	0.874	2.3

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	1.2	56.877	212047	11242	99.994	0.15	0.1495	0.1644	0.1593	0.1702	14.58

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]
1.614			-1.232		-0.382

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.766
r_lrange_it	10.653
r_dihedral_angle_3_deg	10.524
r_lrange_other	9.164
r_dihedral_angle_1_deg	6.935
r_dihedral_angle_2_deg	5.045
r_scangle_it	4.698
r_scangle_other	4.698
r_mcangle_other	4.102
r_mcangle_it	4.1
r_scbond_it	3.108
r_scbond_other	3.107
r_mcbond_it	2.608
r_mcbond_other	2.602
r_rigid_bond_restr	2.3
r_angle_refined_deg	1.489
r_angle_other_deg	0.537
r_nbd_refined	0.212
r_symmetry_nbd_refined	0.197
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.182
r_nbd_other	0.137
r_ncsr_local_group_1	0.121
r_symmetry_xyhbond_nbd_refined	0.112
r_xyhbond_nbd_refined	0.098
r_metal_ion_refined	0.098
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.079
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	4673
Nucleic Acid Atoms
Solvent Atoms	688
Heterogen Atoms	82

Software

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