9RI4 | pdb_00009ri4

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
2.62	53.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.82	α = 90
b = 100.15	β = 90
c = 104.58	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	1.762	72.332	95.8	0.127	0.037	1	12.6	12.2		53224

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	1.762	1.902			1.8	0.49	0.675	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	1.762	72.332	53224	2662	74.948	0.214	0.2117	0.2118	0.2565	0.2564	30.291

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]
0.018			-0.048		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.312
r_dihedral_angle_6_deg	15.162
r_dihedral_angle_2_deg	7.444
r_dihedral_angle_1_deg	7.412
r_lrange_it	7.151
r_scangle_it	5.115
r_mcangle_it	3.8
r_scbond_it	3.619
r_mcbond_it	2.601
r_angle_refined_deg	1.492
r_nbtor_refined	0.312
r_nbd_refined	0.213
r_symmetry_nbd_refined	0.194
r_symmetry_xyhbond_nbd_refined	0.183
r_xyhbond_nbd_refined	0.135
r_ncsr_local_group_1	0.11
r_chiral_restr	0.102
r_metal_ion_refined	0.092
r_gen_planes_refined	0.008
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4648
Nucleic Acid Atoms
Solvent Atoms	268
Heterogen Atoms	49

Software

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