4XKZ

Crystal structure of the C-terminal anticodon loop binding domain of a valyl-tRNA synthetase from Pseudomonas aeruginosa

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	PsaeA.18849.a.B4.PW37589 at 18 mg/mL against Morpheus screen condition B6 10% PEG 8000, 20% ethylene glycol, 0.1 M MOPS-HEPES, pH7.5, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, crystal tracking ID 259627b6, unique puck ID oaf3-9

Crystal Properties
Matthews coefficient	Solvent content
3.44	64.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.36	α = 90
b = 103.36	β = 90
c = 79.14	γ = 90

Symmetry
Space Group	P 4 21 2

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	MARMOSAIC 300 mm CCD		2014-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.95	50	99.3	0.063	0.068	20.8	7.5		31655		-3	31.84

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	100		0.469	0.503	3.75

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.95	50	31655	1585	99.3	0.1576	0.1558	0.1934	RANDOM	35.286

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]
-1.81			-1.81		3.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.421
r_dihedral_angle_4_deg	15.416
r_dihedral_angle_3_deg	13.014
r_dihedral_angle_1_deg	5.253
r_mcangle_it	2.292
r_angle_refined_deg	1.775
r_mcbond_it	1.542
r_mcbond_other	1.537
r_angle_other_deg	1.061
r_chiral_restr	0.115

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.421
r_dihedral_angle_4_deg	15.416
r_dihedral_angle_3_deg	13.014
r_dihedral_angle_1_deg	5.253
r_mcangle_it	2.292
r_angle_refined_deg	1.775
r_mcbond_it	1.542
r_mcbond_other	1.537
r_angle_other_deg	1.061
r_chiral_restr	0.115
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1972
Nucleic Acid Atoms
Solvent Atoms	274
Heterogen Atoms	24

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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.