3SN4

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

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; pH adjusted to 7.0; soaked with 100mM MgCl2 and 100mM alpha-ketoglutarate, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.04	α = 90
b = 105.04	β = 90
c = 144.363	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		2010-08-08	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	1.86	50	99.7	0.084	0.084	29.5	15.2	34329	34226			21.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.89	100		1.4	13.2	1699

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 3GO2	1.86	20	34178	27356	868	80.04	0.1619	0.1606	0.2013	RANDOM	29.2587

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]
-1.27			-1.27		2.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.02
r_dihedral_angle_4_deg	16.011
r_dihedral_angle_3_deg	13.472
r_dihedral_angle_1_deg	5.84
r_scangle_it	3.097
r_scbond_it	1.938
r_angle_refined_deg	1.326
r_mcangle_it	1.068
r_angle_other_deg	0.893
r_mcbond_it	0.578

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.02
r_dihedral_angle_4_deg	16.011
r_dihedral_angle_3_deg	13.472
r_dihedral_angle_1_deg	5.84
r_scangle_it	3.097
r_scbond_it	1.938
r_angle_refined_deg	1.326
r_mcangle_it	1.068
r_angle_other_deg	0.893
r_mcbond_it	0.578
r_mcbond_other	0.153
r_chiral_restr	0.081
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3126
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	13

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	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.