4LC3 | pdb_00004lc3

X-ray crystal structure of a putative UDP-4-amino-4-deoxy-l-arabinose--oxoglutarate aminotransferase from Burkholderia cenocepacia

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MDO	PDB ENTRY 1MDO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	289	20% PEG6000, 100 mM sodium citrate tribasic, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 190.93	α = 90
b = 58.91	β = 97.39
c = 83.08	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		2013-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.9786	APS	21-ID-G

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	1.6	50	97.2	0.063	15.62		120854	117470		-3	18.906

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	1.6	1.64	95.6		0.371	3.58

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 1MDO	1.6	47.38	120854	117469	5918	97.18	0.113	0.1111	0.13	0.1479	0.16	RANDOM	14.0425

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]
-0.14		-0.31	0.21		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	33.609
r_dihedral_angle_2_deg	29.294
r_dihedral_angle_4_deg	14.632
r_dihedral_angle_3_deg	11.605
r_sphericity_bonded	9.723
r_dihedral_angle_1_deg	5.733
r_rigid_bond_restr	2.521
r_mcangle_it	1.552
r_angle_refined_deg	1.407
r_mcbond_it	1.286

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	33.609
r_dihedral_angle_2_deg	29.294
r_dihedral_angle_4_deg	14.632
r_dihedral_angle_3_deg	11.605
r_sphericity_bonded	9.723
r_dihedral_angle_1_deg	5.733
r_rigid_bond_restr	2.521
r_mcangle_it	1.552
r_angle_refined_deg	1.407
r_mcbond_it	1.286
r_mcbond_other	1.277
r_angle_other_deg	0.811
r_chiral_restr	0.16
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5774
Nucleic Acid Atoms
Solvent Atoms	1016
Heterogen Atoms	74

Software

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

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.