9VCI | pdb_00009vci

Crystal structure of Escherichia coli tryptophanyl-tRNA synthetase in complex with an inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8I1Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		290	0.15 M ammonium sulfate, 0.1 M HEPES pH 7.5, 25% w/v PEG 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.495	α = 90
b = 79.532	β = 105.82
c = 77.651	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS 6M		2024-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97861	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.88	59.16	98.5	0.086	13.6	6.4		57750

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.88	1.98			0.653

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.88	59.16	54869	2861	98.8	0.19503	0.19381	0.1966	0.2183	0.2195	RANDOM	25.82

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]
-2.27		0.07	1.7		0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.028
r_dihedral_angle_4_deg	19.325
r_dihedral_angle_3_deg	12.455
r_dihedral_angle_1_deg	5.435
r_long_range_B_refined	4.166
r_long_range_B_other	4.139
r_scangle_other	3.649
r_scbond_it	2.87
r_scbond_other	2.814
r_mcangle_it	2.563
r_mcangle_other	2.563
r_angle_other_deg	2.349
r_mcbond_it	2.065
r_mcbond_other	2.064
r_angle_refined_deg	1.742
r_chiral_restr	0.101
r_bond_other_d	0.036
r_bond_refined_d	0.015
r_gen_planes_other	0.007
r_gen_planes_refined	0.006
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5000
Nucleic Acid Atoms
Solvent Atoms	506
Heterogen Atoms	110

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
MOLREP	phasing