9RHX | pdb_00009rhx

SARS-CoV-2 main protease with a bound inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		in-hoiuse structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.11	α = 90
b = 99.25	β = 90
c = 103.98	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 EIGER X 16M		2023-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00	SLS	X10SA

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	1.62	71.794	94.4	0.165	1	13.1	13.1		72324

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	1.62	1.75			0.41	1.7

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	1.62	71.794	72324	3688	80.192	0.196	0.1946	0.1946	0.2227	0.2225	26.823

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]
			-0.015		0.015

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.191
r_dihedral_angle_6_deg	16.055
r_dihedral_angle_2_deg	9.978
r_lrange_other	7.625
r_lrange_it	7.624
r_dihedral_angle_1_deg	7.099
r_scangle_it	6.074
r_scangle_other	6.073
r_scbond_it	3.932
r_scbond_other	3.931
r_mcangle_other	3.626
r_mcangle_it	3.625
r_mcbond_it	2.546
r_mcbond_other	2.545
r_dihedral_angle_other_3_deg	2.205
r_angle_refined_deg	1.56
r_angle_other_deg	0.527
r_symmetry_nbd_refined	0.228
r_nbd_refined	0.219
r_nbd_other	0.206
r_symmetry_xyhbond_nbd_refined	0.193
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.136
r_ncsr_local_group_1	0.121
r_metal_ion_refined	0.108
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.078
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	4697
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	44

Software

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