3GO2

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

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.8	294	100mM Sodium acetate pH 4.8, 2.4M Sodium formate, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.697	α = 90
b = 104.697	β = 90
c = 145.828	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	MAR CCD 165 mm		2008-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

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	1.7	85.126	99.8	0.058	0.058	26	9	44736	44736			16.1

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	1.7	1.79	99		0.251	0.251	6.8	8	6380

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1.7	20	44235	44235	2230	98.76	0.153	0.152	0.185	RANDOM	18.962

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]
-0.21			-0.21		0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.927
r_dihedral_angle_4_deg	16.815
r_dihedral_angle_3_deg	11.387
r_dihedral_angle_1_deg	5.708
r_scangle_it	3.434
r_scbond_it	2.159
r_angle_refined_deg	1.333
r_mcangle_it	1.243
r_angle_other_deg	0.888
r_mcbond_it	0.685

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.927
r_dihedral_angle_4_deg	16.815
r_dihedral_angle_3_deg	11.387
r_dihedral_angle_1_deg	5.708
r_scangle_it	3.434
r_scbond_it	2.159
r_angle_refined_deg	1.333
r_mcangle_it	1.243
r_angle_other_deg	0.888
r_mcbond_it	0.685
r_mcbond_other	0.205
r_chiral_restr	0.08
r_bond_refined_d	0.013
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	3069
Nucleic Acid Atoms
Solvent Atoms	387
Heterogen Atoms	2

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXCD	phasing
SHELXE	model building

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.