3LA9 | pdb_00003la9

Crystal structure of the trimeric autotransporter adhesin head domain BpaA from Burkholderia pseudomallei, iodide phased

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	289	Original hit: PACT B1, 0.1 M MIB buffer pH 4.0, 25% PEG 1500; soaked into 0.1 M MIB buffer pH 4.0, 1.0 M KI, 35% PEG 1500 for 1 hour; crystal tracking ID 203140b1, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.737879	29.224056

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.78	α = 90
b = 50.78	β = 90
c = 135.66	γ = 120

Symmetry
Space Group	H 3

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+		2009-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	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	2.05	50	99.5	0.025	53.75	5.43		8173		-3	13.559

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)
	2.05	2.1	96		0.039	31	3.62	1196

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	SAD	THROUGHOUT	2.05	45.22	8173	377	99.57	0.117	0.115	0.15	0.154	0.2	RANDOM	7.779

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]
0.73			0.73		-1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.471
r_dihedral_angle_4_deg	29.368
r_dihedral_angle_3_deg	10.11
r_dihedral_angle_1_deg	5.924
r_scangle_it	1.913
r_scbond_it	1.236
r_angle_refined_deg	1.142
r_mcangle_it	0.919
r_mcbond_it	0.54
r_chiral_restr	0.078

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.471
r_dihedral_angle_4_deg	29.368
r_dihedral_angle_3_deg	10.11
r_dihedral_angle_1_deg	5.924
r_scangle_it	1.913
r_scbond_it	1.236
r_angle_refined_deg	1.142
r_mcangle_it	0.919
r_mcbond_it	0.54
r_chiral_restr	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1124
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	9

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.