9RI3 | pdb_00009ri3

SARS-CoV-2 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	53.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.94	α = 90
b = 100.9	β = 90
c = 104.84	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)	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	1.723	72.7	92.8	0.138	0.057	1	13.4	13.1		55891

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	1.723	1.884			2.1	0.6	0.451	1.6

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	1.723	72.7	55891	2879	72.736	0.212	0.2104	0.2105	0.2383	0.2378	34.064

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]
-0.001			-0.009		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.603
r_dihedral_angle_6_deg	15.727
r_dihedral_angle_2_deg	10.31
r_lrange_other	8.255
r_lrange_it	8.252
r_dihedral_angle_1_deg	7.577
r_scangle_it	6.395
r_scangle_other	6.394
r_mcangle_other	4.341
r_mcangle_it	4.34
r_scbond_it	4.14
r_scbond_other	4.139
r_mcbond_it	3.036
r_mcbond_other	3.035
r_angle_refined_deg	1.43
r_angle_other_deg	0.485
r_nbd_refined	0.217
r_symmetry_xyhbond_nbd_refined	0.197
r_symmetry_nbd_refined	0.194
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.183
r_nbd_other	0.164
r_metal_ion_refined	0.162
r_xyhbond_nbd_refined	0.135
r_ncsr_local_group_1	0.114
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.07
r_symmetry_xyhbond_nbd_other	0.021
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_dihedral_angle_other_3_deg	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4715
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	45

Software

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