3SN1

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GO2	pdb entry 3GO2

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 2mM tartrate , VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.932	α = 90
b = 104.932	β = 90
c = 145.145	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	1.8	50	99.9	0.103	0.103	23	15.9	37833	37795			18.8

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	1.8	1.83	100		0.71	4.5	15.6	1857

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	1.8	20	37776	37617	1172	99.58	0.1419	0.1412	0.1648	RANDOM	19.2069

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]
0.05			0.05		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.834
r_dihedral_angle_4_deg	21.136
r_dihedral_angle_3_deg	12.632
r_dihedral_angle_1_deg	5.694
r_scangle_it	2.919
r_scbond_it	1.82
r_angle_refined_deg	1.266
r_mcangle_it	1.03
r_angle_other_deg	0.884
r_mcbond_it	0.556

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.834
r_dihedral_angle_4_deg	21.136
r_dihedral_angle_3_deg	12.632
r_dihedral_angle_1_deg	5.694
r_scangle_it	2.919
r_scbond_it	1.82
r_angle_refined_deg	1.266
r_mcangle_it	1.03
r_angle_other_deg	0.884
r_mcbond_it	0.556
r_mcbond_other	0.168
r_chiral_restr	0.078
r_bond_refined_d	0.012
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	274
Heterogen Atoms	14

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 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.