3OO9 | pdb_00003oo9

Crystal structures and biochemical characterization of the bacterial solute receptor AcbH reveal an unprecedented exclusive substrate preference for b-D-galactopyranose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		model from SeMet SAD phasing

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	291	2.2M (NH4)2SO4, 100mM citric acid , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.25	α = 90
b = 65.76	β = 90.03
c = 177.72	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	ADSC QUANTUM 210	mirrors	2010-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.91841	BESSY	14.2

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	1.76	33.71	94.4	0.092	8.78	2.8		84900		-3	20.134

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.76	1.81	88.7		0.553	0.69	1.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	model from SeMet SAD phasing	1.76	33.71	84899	4245	100	0.157	0.155	0.16	0.1948	0.2	RANDOM	14.5202

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]
-0.99		-0.3	0.61		0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.601
r_dihedral_angle_4_deg	19.044
r_dihedral_angle_3_deg	13.172
r_dihedral_angle_1_deg	5.642
r_scangle_it	5.407
r_scbond_it	3.651
r_mcangle_it	2.115
r_mcbond_it	1.405
r_angle_refined_deg	1.359
r_chiral_restr	0.114

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.601
r_dihedral_angle_4_deg	19.044
r_dihedral_angle_3_deg	13.172
r_dihedral_angle_1_deg	5.642
r_scangle_it	5.407
r_scbond_it	3.651
r_mcangle_it	2.115
r_mcbond_it	1.405
r_angle_refined_deg	1.359
r_chiral_restr	0.114
r_bond_refined_d	0.013
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6166
Nucleic Acid Atoms
Solvent Atoms	1004
Heterogen Atoms	133

Software

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

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.