Experiment: 9KVC

Crystal structure of tryptophanyl-tRNA synthetase from Staphylococcus aureus

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-P67594-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	291	0.1 M Tris, 5% gamma-PGA (Na salt, low molecular), 20% PEG 2000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 186.251	α = 90
b = 69.713	β = 101.684
c = 98.441	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 PILATUS3 6M		2024-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97907	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	3.04	91.2	98.8	0.158	9.3	5.7		23734			53.14

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	3.04	3.2			0.629

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.04	65.12	1.35	23678	1999	98.33	0.2111	0.2093	0.2094	0.2297	0.2293	60.6

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	8.2558
f_angle_d	1.2533
f_chiral_restr	0.0642
f_plane_restr	0.0209
f_bond_d	0.0097

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7504
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	21

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing