4OVQ

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM ROSEOBACTER DENITRIFICANS, TARGET EFI-510230, WITH BOUND BETA-D-GLUCURONATE


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7298Protein (33.12 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 1 mM D-Glucuronate); Reservoir (0.2M Calcium Acetate 0.1 M Tris pH 7.0 20 %(w/v) PEG 3000); Cryoprotection (20% glycerol, 80% Reservoir)
Crystal Properties
Matthews coefficientSolvent content
2.244.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.209α = 90
b = 78.209β = 90
c = 134.424γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEMIRRORS2013-11-26SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-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
11.510099.90.0739.311.54897411.94
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5310011.32406

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-VALUE1.50125.1481.9746513236294.880.18090.17930.210721.0291
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_d12.796
f_angle_d1.325
f_chiral_restr0.079
f_bond_d0.012
f_plane_restr0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2303
Nucleic Acid Atoms
Solvent Atoms332
Heterogen Atoms14

Software

Software
Software NamePurpose
HKL-3000phasing
PHENIXrefinement