4YWH | pdb_00004ywh

CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM ACTINOBACILLUS SUCCINOGENES 130Z (Asuc_0499, TARGET EFI-511068) WITH BOUND D-XYLOSE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4MA0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	Protein (10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-Xylose); Reservoir (MCSG1 G4)(0.2 M Potassium Sodium Tartrate, 20 %(w/v) PEG 3350); Cryoprotection (20% Ethylene Glycol, 80% Reservoir)

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.796	α = 90
b = 37.67	β = 91.5
c = 105.336	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	RAYONIX MX225HE	MIRRORS	2015-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.35	24.838	97.6	0.083	0.093	0.04	9	5		26617			31.31

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.39	89.7		0.75	0.855	0.399	0.764		3.9	1190

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4MA0	2.35	24.838	1.34	25700	1209	93.17	0.1607	0.1567	0.16	0.2382	0.24	41.2848

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
f_dihedral_angle_d	15.276
f_angle_d	1.41
f_chiral_restr	0.058
f_bond_d	0.014
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4684
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	20

Software

Software
Software Name	Purpose
HKL-3000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MOLREP	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.