4YZZ

Crystal structure of a TRAP transporter solute binding protein (IPR025997) from Bordetella bronchiseptica RB50 (BB0280, TARGET EFI-500035) mixed occupancy dimer, copurified calcium and picolinate bound active site versus apo site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4YIC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.5298Protein (10 mM HEPES pH 7.5, 5 mM DTT, 1mM CaCl2, 1 mM Picolinic Acid); Reservoir (MCSG2 (E8) 0.1 M CHES pH 9.5, 20 %(w/v) PEG 8000); Cryoprotection (20% diethylene glycol, 80% Reservoir)
Crystal Properties
Matthews coefficientSolvent content
1.8433.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.249α = 90
b = 50.104β = 104.47
c = 96.556γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEMIRRORS2015-02-11MSINGLE 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)Rpim I (All)CC (Half)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
11.325.4295.20.0760.0450.99811.53.81388369.57
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.3280.60.5830.3580.7972.13.35808

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4YIC1.324.1981.34138794681294.910.140.13880.16314.725
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_d13.229
f_angle_d1.273
f_chiral_restr0.071
f_bond_d0.008
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5240
Nucleic Acid Atoms
Solvent Atoms920
Heterogen Atoms37

Software

Software
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction