4E51

Crystal structure of a histidyl-tRNA synthetase HisRS from Burkholderia thailandensis bound to histidine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	ButhA.00063.a.A1 PS01164 at 31 mg/mL with 5 mM L-histidine against Wizard III A3 focus screen, 350 mM magnesium formate, 12% PEG 3350 with 20% glycerol as cryo-protectant, crystal tracking ID 230808g3, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.16	α = 90
b = 116.36	β = 90
c = 142.99	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	CCD	ADSC QUANTUM 315r		2012-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.976484	ALS	5.0.3

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	2.65	50	99.5	0.065	24.34	7.8	34582	34582		-3	56.022

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	2.65	2.72	99.9		0.524	4.22

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1HTT	2.65	19.61	34582	1742	99.46	0.2078	0.206	0.2404	RANDOM	51.8046

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]
-3.91			5.78		-1.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.258
r_dihedral_angle_4_deg	25.247
r_dihedral_angle_3_deg	15.453
r_dihedral_angle_1_deg	6.374
r_angle_refined_deg	1.464
r_angle_other_deg	1.13
r_chiral_restr	0.075
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.258
r_dihedral_angle_4_deg	25.247
r_dihedral_angle_3_deg	15.453
r_dihedral_angle_1_deg	6.374
r_angle_refined_deg	1.464
r_angle_other_deg	1.13
r_chiral_restr	0.075
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6041
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	22

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.