9RJ5 | pdb_00009rj5

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
2.78	55.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.8	α = 90
b = 81.76	β = 114.674
c = 51.72	γ = 90

Symmetry
Space Group	C 1 2 1

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		2023-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.0	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	1.244	47.004	95.4	0.043	0.027	1	12.4	3.4		85942

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	1.244	1.304			0.379	0.258	0.858	2.2

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	THROUGHOUT	1.25	47.004	84289	4118	82.684	0.152	0.1509	0.159	0.1764	0.182	23.515

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]
-2.048		0.918	-2.332		2.486

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.151
r_dihedral_angle_4_deg	15.809
r_dihedral_angle_3_deg	11.952
r_dihedral_angle_1_deg	7.049
r_rigid_bond_restr	6.34
r_lrange_it	4.618
r_lrange_other	4.532
r_scangle_it	4.294
r_scangle_other	4.293
r_scbond_it	3.929
r_scbond_other	3.929
r_mcangle_other	3.096
r_mcangle_it	3.079
r_mcbond_it	2.495
r_mcbond_other	2.413
r_angle_refined_deg	1.815
r_angle_other_deg	1.458
r_nbd_refined	0.225
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.163
r_symmetry_xyhbond_nbd_refined	0.163
r_nbd_other	0.155
r_symmetry_nbd_refined	0.108
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2289
Nucleic Acid Atoms
Solvent Atoms	281
Heterogen Atoms	22

Software

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