9RI8 | pdb_00009ri8

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
2.57	52.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.9	α = 90
b = 99.2	β = 90
c = 103.38	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		2023-06-02	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	1.781	71.6	95.1	0.198	0.056	1	11.9	13.4		55779

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	1.781	1.919			1.965	0.552	0.504	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	1.781	71.577	55779	2853	82.659	0.22	0.2185	0.2186	0.2501	0.25	32.268

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]
-0.099			0.28		-0.181

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.457
r_dihedral_angle_3_deg	13.777
r_lrange_it	10.546
r_lrange_other	10.545
r_dihedral_angle_1_deg	7.629
r_scangle_it	6.122
r_scangle_other	6.122
r_dihedral_angle_2_deg	5.686
r_mcangle_it	4.689
r_mcangle_other	4.688
r_scbond_it	3.809
r_scbond_other	3.808
r_mcbond_it	3.012
r_mcbond_other	3.012
r_angle_refined_deg	1.494
r_angle_other_deg	0.535
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.215
r_nbd_other	0.208
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.182
r_metal_ion_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.167
r_symmetry_nbd_refined	0.165
r_ncsr_local_group_1	0.112
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.079
r_symmetry_xyhbond_nbd_other	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4723
Nucleic Acid Atoms
Solvent Atoms	278
Heterogen Atoms	33

Software

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