3S6L | pdb_00003s6l

Crystal structure of a YadA-like head domain of the trimeric autotransporter adhesin BoaA from Burkholderia pseudomallei solved by iodide ion SAD phasing

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	289	BupsA.01663.c.A9 at 22.5 mg/mL against JCSG+ screen E7 focus screen, 6% isopropanol, 0.1 M Na cacodylate pH 6.9, 0.2 M ZnCl2 soaked with 6% isopropanol, 0.1 M Na cacodylate pH 7.5, 0.2 M ZnCl2, 0.7 M NaI, 22% ethylene glycol for 1 minute, crystal tracking ID 218438h2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144	α = 90
b = 144	β = 90
c = 144	γ = 90

Symmetry
Space Group	P 21 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+	VariMax	2011-04-06	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	2.3	50	99.9	0.125	17.43	12.1	44378	44337		-3	31.861

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	2.3	2.36	100		0.633	4.66	12.1	3252

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	2.3	50	44216	2222	99.67	0.1764	0.1748	0.18	0.2072	0.21	RANDOM	24.8705

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.368
r_dihedral_angle_4_deg	20.924
r_dihedral_angle_3_deg	12.09
r_dihedral_angle_1_deg	5.172
r_scangle_it	3.363
r_scbond_it	2.143
r_angle_refined_deg	1.346
r_mcangle_it	1.071
r_mcbond_it	0.597
r_chiral_restr	0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.368
r_dihedral_angle_4_deg	20.924
r_dihedral_angle_3_deg	12.09
r_dihedral_angle_1_deg	5.172
r_scangle_it	3.363
r_scbond_it	2.143
r_angle_refined_deg	1.346
r_mcangle_it	1.071
r_mcbond_it	0.597
r_chiral_restr	0.09
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4929
Nucleic Acid Atoms
Solvent Atoms	330
Heterogen Atoms	95

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
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.