2OO6

Crystal structure of putative L-alanine-DL-glutamate epimerase from Burkholderia xenovorans strain LB400

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	294	100mM Tris-HCl pH 8.5, 12% Glycerol, 1.5M Ammonium sulfate, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.906	α = 90
b = 104.906	β = 90
c = 145.658	γ = 90

Symmetry
Space Group	I 4 2 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	ADSC QUANTUM 315		2007-01-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.97958	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.8	85.13	93.2	0.109	0.109	16.8	8.8		35232			22.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	56.8		0.825	0.825	0.9	2.3	3054

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	SAD	THROUGHOUT	1.8	20	35192	1755	93.05	0.157	0.156	0.192	RANDOM	26.362

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]
-0.23			-0.23		0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.403
r_dihedral_angle_4_deg	19.024
r_dihedral_angle_3_deg	12.007
r_dihedral_angle_1_deg	5.548
r_scangle_it	3.352
r_scbond_it	2.158
r_angle_refined_deg	1.331
r_mcangle_it	1.231
r_mcbond_it	0.78
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.403
r_dihedral_angle_4_deg	19.024
r_dihedral_angle_3_deg	12.007
r_dihedral_angle_1_deg	5.548
r_scangle_it	3.352
r_scbond_it	2.158
r_angle_refined_deg	1.331
r_mcangle_it	1.231
r_mcbond_it	0.78
r_nbtor_refined	0.312
r_symmetry_hbond_refined	0.236
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.19
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.094
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3103
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms	10

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing

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.