4EGQ

Crystal structure of D-alanine-D-alanine ligase B from Burkholderia pseudomallei

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5	289	BupsA.00119.a.A1 PW25270 at 30.8 mg/mL against Wizard Full screen condition D2, 1 M NaK Tartrate, 0.1 M CHES pH 9.5, 0.2 M Li2SO4, crystal tracking ID 203378d2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.389	α = 84.47
b = 66.092	β = 80.5
c = 98.558	γ = 83.59

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100				2008-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97946	APS	24-ID-E

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	2.2	50	97.8	0.124	9.437	3.7		54908

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	2.2	2.24	96.6		0.546		3.1	2703

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 4EG0	2.2	35.27	54818	2772	97.02	0.2118	0.2097	0.2503	RANDOM	38.9073

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]
-0.37	-0.04	1.48	-0.69	0.59	0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.622
r_dihedral_angle_4_deg	18.491
r_dihedral_angle_3_deg	13.126
r_dihedral_angle_1_deg	5.395
r_angle_refined_deg	1.472
r_angle_other_deg	1.411
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.622
r_dihedral_angle_4_deg	18.491
r_dihedral_angle_3_deg	13.126
r_dihedral_angle_1_deg	5.395
r_angle_refined_deg	1.472
r_angle_other_deg	1.411
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.007
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8399
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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 R01GM133198.