4KZK

The structure of the periplasmic L-arabinose binding protein from Burkholderia thailandensis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ABP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	50% MPD, 200mM Ammonium Phosphate, 100mM Tris pH8.5, 14.8mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.77	α = 90
b = 51.82	β = 107.34
c = 59.22	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MARMOSAIC 225 mm CCD		2013-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97857	APS	21-ID-F

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	1.5	43.73	100	0.111	21.42			11596		-3	20.707

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	1.95	2	100		0.437	6.75

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	5ABP	1.5	43.73	2142	99.66	0.1708	0.1696	0.1925	RANDOM	17.7108

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]
-0.15		-0.84	-0.25		0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.811
r_dihedral_angle_4_deg	15.924
r_dihedral_angle_3_deg	11.448
r_dihedral_angle_1_deg	5.305
r_angle_refined_deg	1.272
r_mcangle_it	0.772
r_angle_other_deg	0.766
r_mcbond_it	0.458
r_mcbond_other	0.446
r_chiral_restr	0.072

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.811
r_dihedral_angle_4_deg	15.924
r_dihedral_angle_3_deg	11.448
r_dihedral_angle_1_deg	5.305
r_angle_refined_deg	1.272
r_mcangle_it	0.772
r_angle_other_deg	0.766
r_mcbond_it	0.458
r_mcbond_other	0.446
r_chiral_restr	0.072
r_bond_refined_d	0.008
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	2235
Nucleic Acid Atoms
Solvent Atoms	344
Heterogen Atoms	12

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.