4IFW

Crystal structure of Treponema pallidum TP0796 Flavin trafficking protein, ADP inhibited form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4IFUPDB ENTRY 4IFU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging-drop vapor diffusion6.52930.1 M MES, 0.8 M sodium acetate, 0.1 M NaCl, 20% (w/v) ethylene glycol;, pH 6.5, hanging-drop vapor diffusion, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1241.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.829α = 90
b = 47.252β = 102.03
c = 57.643γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmonochromator2011-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97918APS19-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
12.350990.1347.13.9137661376611
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)
12.32.3494.90.3883.4

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISPDB ENTRY 4IFU2.300129.6541.36137181372167398.750.17980.17680.23821.1165
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_d14.794
f_angle_d0.795
f_chiral_restr0.043
f_bond_d0.013
f_plane_restr0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2500
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms29

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
DENZOdata reduction
HKL-3000data scaling
PHENIXphasing