3SN0 | pdb_00003sn0

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

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 100mM fumarate, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.75	α = 90
b = 104.75	β = 90
c = 144.885	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	99.5	0.115	0.115	18.6	15.6	37586	37398			18.1

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	1.8	1.83	100		0.558	0.558	4.6	15.4	1862

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 3GO2	1.8	20	37586	37211	1164	99	0.1435	0.1429	0.16	0.1647	0.18	RANDOM	18.4829

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		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.229
r_dihedral_angle_4_deg	16.824
r_dihedral_angle_3_deg	12.052
r_dihedral_angle_1_deg	5.737
r_scangle_it	3.001
r_scbond_it	1.871
r_angle_refined_deg	1.228
r_mcangle_it	1.1
r_angle_other_deg	0.871
r_mcbond_it	0.587

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.229
r_dihedral_angle_4_deg	16.824
r_dihedral_angle_3_deg	12.052
r_dihedral_angle_1_deg	5.737
r_scangle_it	3.001
r_scbond_it	1.871
r_angle_refined_deg	1.228
r_mcangle_it	1.1
r_angle_other_deg	0.871
r_mcbond_it	0.587
r_mcbond_other	0.161
r_chiral_restr	0.077
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	3173
Nucleic Acid Atoms
Solvent Atoms	296
Heterogen Atoms	11

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.