4YIC

CRYSTAL STRUCTURE OF A TRAP TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM BORDETELLA BRONCHISEPTICA RB50 (BB0280, TARGET EFI-500035) WITH BOUND PICOLINIC ACID


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HZLPDB entry 2HZL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7298Protein (10 mM HEPES pH 7.5, 5 mM DTT, 1mM CaCl2, 1 mM Picolinic Acid); Reservoir ((MCSG2 B7 D3)(0.1 M Bis-Tris Propane pH 7.0, 2.8 M Sodium Acetate pH 7.0)); Cryoprotection (20% glycerol, 80% Reservoir)
Crystal Properties
Matthews coefficientSolvent content
2.3347.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.681α = 90
b = 86.141β = 100.86
c = 72.339γ = 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
11.627.1599.40.0660.040.99810.73.710193119.81
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)
11.61.6398.80.8350.5010.7151.63.74994

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-VALUEPDB entry 2HZL1.625.5621.34101764501199.20.14420.14270.172932.2181
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_d13.393
f_angle_d1.213
f_chiral_restr0.05
f_bond_d0.01
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5360
Nucleic Acid Atoms
Solvent Atoms735
Heterogen Atoms51

Software

Software
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing