4Z0N

Crystal Structure of a Periplasmic Solute binding protein (IPR025997) from Streptobacillus moniliformis DSM-12112 (Smon_0317, TARGET EFI-511281) with bound D-Galactose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.5298Protein (20 mM HEPES, pH 7.5, 5 mM DTT, 10 mM D-Galactose); Reservoir (0.1 M Sodium acetate:HCl pH 4.5, 2.0 M Ammonium sulfate); Cryoprotection (80% 2M Lithium sulfate, 20% Reservoir
Crystal Properties
Matthews coefficientSolvent content
2.0540.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.396α = 90
b = 44.011β = 104.32
c = 62.037γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEMIRRORS2015-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97931APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.265088.570.092817338414.37

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONSADFREE R-VALUE1.2624.1151.3469792359388.590.13990.13860.16519.8511
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.078
f_angle_d1.039
f_chiral_restr0.071
f_bond_d0.005
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2375
Nucleic Acid Atoms
Solvent Atoms451
Heterogen Atoms63

Software

Software
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing