9RI0 | pdb_00009ri0

SARS-CoV-2 3CL 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-house 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
2.66	53.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.86	α = 90
b = 101.85	β = 90
c = 104.25	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	1.39	72.853	96.3	0.08	1	12.7	6.6		767039

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.39	1.497			0.696	0.599	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	1.39	72.853	116189	5633	79.903	0.177	0.1763	0.1763	0.198	0.1979	16.012

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]
-0.005			0.017		-0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.947
r_dihedral_angle_3_deg	14.436
r_dihedral_angle_1_deg	6.921
r_dihedral_angle_2_deg	6.587
r_lrange_it	5.917
r_lrange_other	5.917
r_scangle_it	4.627
r_scangle_other	4.622
r_scbond_it	3.122
r_scbond_other	3.119
r_mcangle_other	2.31
r_mcangle_it	2.309
r_angle_refined_deg	1.715
r_mcbond_it	1.626
r_mcbond_other	1.626
r_angle_other_deg	0.578
r_nbd_refined	0.219
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.184
r_symmetry_nbd_refined	0.157
r_nbd_other	0.157
r_xyhbond_nbd_refined	0.143
r_metal_ion_refined	0.132
r_ncsr_local_group_1	0.129
r_symmetry_xyhbond_nbd_refined	0.128
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.083
r_dihedral_angle_other_3_deg	0.022
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4701
Nucleic Acid Atoms
Solvent Atoms	604
Heterogen Atoms	85

Software

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