9RJ8 | pdb_00009rj8

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
2.65	53.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.802	α = 90
b = 101.812	β = 90
c = 103.946	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		2022-10-03	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	1.433	72.735	94.9	0.065	0.027	1	13	6.6		98276

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	1.433	1.543			1.034	0.441	0.584	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	THROUGHOUT	1.433	72.735	98276	4952	74.275	0.162	0.1594	0.1672	0.2168	0.2192	28.676

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]
0.687			-0.793		0.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.122
r_dihedral_angle_3_deg	14.697
r_dihedral_angle_2_deg	10.718
r_rigid_bond_restr	8.919
r_lrange_it	7.863
r_lrange_other	7.816
r_scangle_it	7.72
r_scangle_other	7.72
r_scbond_it	7.355
r_scbond_other	7.353
r_dihedral_angle_1_deg	7.215
r_mcangle_other	6.847
r_mcangle_it	6.846
r_mcbond_it	5.895
r_mcbond_other	5.877
r_angle_refined_deg	1.509
r_angle_other_deg	0.532
r_symmetry_nbd_refined	0.23
r_nbd_refined	0.206
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.154
r_nbd_other	0.153
r_xyhbond_nbd_refined	0.139
r_ncsr_local_group_1	0.117
r_symmetry_xyhbond_nbd_other	0.096
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4639
Nucleic Acid Atoms
Solvent Atoms	410
Heterogen Atoms	58

Software

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