4PC9

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM ROSENBACTER DENITRIFICANS OCh 114 (RD1_1052, TARGET EFI-510238) WITH BOUND D-MANNONATE


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5298Protein (42.4 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-MANNONATE); Reservoir (0.1 M Tris pH 8.5, 2.4 M di-Ammonium Phosphate); Cryoprotection (80% Reservoir + 20% diethylene glycol)
Crystal Properties
Matthews coefficientSolvent content
2.0239

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.365α = 90
b = 73.339β = 90
c = 75.752γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEMIRRORS2014-04-02MSINGLE 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
11.375.7599.70.11717.814.1722378.67
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.3299.30.9184.113.6

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 DIFFRACTIONSADNONE1.323.8751.34138252698999.680.13560.13490.148413.55
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_d13.755
f_angle_d1.213
f_chiral_restr0.07
f_bond_d0.012
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2310
Nucleic Acid Atoms
Solvent Atoms445
Heterogen Atoms24

Software

Software
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
PDB_EXTRACTdata extraction
Aimlessdata scaling