4EGJ

Crystal structure of D-alanine-D-alanine ligase from Burkholderia xenovorans

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EG0	pdb entry 3eg0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	Qiagen JCSG Core1 screen d5: 20% PEG 3350, 200mM LiCl; BuxeA.00119.a.A1 PS01358 at 23.2mg/ml, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.93	α = 90
b = 78.93	β = 90
c = 224.74	γ = 90

Symmetry
Space Group	P 43

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	RIGAKU SATURN 944+		2012-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.3	50	97.8	0.078	10.11	2.5	60791	59426		-3	36.882

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	2.3	2.36	99.3		0.478	0.478	2.09	2.4	4463

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 3eg0	2.3	49.99	60791	59384	3006	97.8	0.2254	0.2254	0.2236	0.2597	RANDOM	32.5859

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]
0.45			0.45		-0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.944
r_dihedral_angle_4_deg	19.567
r_dihedral_angle_3_deg	13.747
r_dihedral_angle_1_deg	5.94
r_angle_refined_deg	1.698
r_angle_other_deg	1.473
r_chiral_restr	0.095
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.944
r_dihedral_angle_4_deg	19.567
r_dihedral_angle_3_deg	13.747
r_dihedral_angle_1_deg	5.94
r_angle_refined_deg	1.698
r_angle_other_deg	1.473
r_chiral_restr	0.095
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.008
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8047
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms

Software

Software
Software Name	Purpose
JDirector	data collection
PHASER	phasing
REFMAC	refinement
XSCALE	data scaling

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.