4Q1T | pdb_00004q1t

Crystal structure of a glutamate 5-kinase from Burkholderia thailandensis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J5T	PDB ENTRY 2J5T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	ButhA.00483.a.A1.PW33346 at 40 mg/mL against PACT screen condition F7, 0.2 M NaOAc, 0.1 M BisTris Propane pH 6.5, 20% PEG 3350 supplemented with 20% ethylene glycol as cryo-protectant, crystal tracking ID 226003f7, unique puck ID gzd6-4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.85	α = 90
b = 69.15	β = 119.51
c = 141.68	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	CCD	MARMOSAIC 300 mm CCD		2012-02-03	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)	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	2.15	50	99.6	0.069	13.25	4.6	69894	69634		-3	45.726

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	2.15	2.21	99.9		0.491	2.81

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2J5T	2.15	50	69634	3519	99.79	0.2205	0.2193	0.22	0.2434	0.25	RANDOM	42.55

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]
-1.11		-1.69	1.83		0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.068
r_dihedral_angle_4_deg	19.122
r_dihedral_angle_3_deg	13.795
r_dihedral_angle_1_deg	5.103
r_mcangle_it	2.797
r_mcbond_it	1.704
r_mcbond_other	1.704
r_angle_refined_deg	1.314
r_angle_other_deg	1.21
r_chiral_restr	0.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.068
r_dihedral_angle_4_deg	19.122
r_dihedral_angle_3_deg	13.795
r_dihedral_angle_1_deg	5.103
r_mcangle_it	2.797
r_mcbond_it	1.704
r_mcbond_other	1.704
r_angle_refined_deg	1.314
r_angle_other_deg	1.21
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_bond_other_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9885
Nucleic Acid Atoms
Solvent Atoms	279
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
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 R01GM157729.