4NN3

Crystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio salexigens (Desal_2161), Target EFI-510109, with bound orotic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSTRUCTURE SOLVED INITIALLY IN SAME CRYSTAL FORM SOAKED WITH SODIUM IODIDE AND SAD PHASED

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529840.2 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, reservoir: MCSG1(H9) (0.1 M Bis-Tris, pH 5.5, 25% w/v PEG3350), cryoprotection: 4:1 50% w/v PEG3350:reservoir, ligand copurified with protein, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.7830.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.346α = 90
b = 147.006β = 90
c = 39.272γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEmirrors2013-11-08MSINGLE 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)R Sym 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
11.4147.00693.60.0660.06614.95.5534945349410.45
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4884.70.60.61.34.46914

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISSTRUCTURE SOLVED INITIALLY IN SAME CRYSTAL FORM SOAKED WITH SODIUM IODIDE AND SAD PHASED1.430.7285341953419272693.220.15470.15470.15290.1886RANDOM16.6572
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_d15.913
f_angle_d1.232
f_chiral_restr0.061
f_bond_d0.009
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2451
Nucleic Acid Atoms
Solvent Atoms434
Heterogen Atoms22

Software

Software
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
PHENIXphasing