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Crystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio salexigens (Desal_2161), Target EFI-510109, with bound orotic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other STRUCTURE SOLVED INITIALLY IN SAME CRYSTAL FORM SOAKED WITH SODIUM IODIDE AND SAD PHASED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 40.2 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 coefficient Solvent content 1.78 30.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.346 α = 90 b = 147.006 β = 90 c = 39.272 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX225HE mirrors 2013-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.4 147.006 93.6 0.066 0.066 14.9 5.5 53494 53494 10.45
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) Redundancy Number Unique Reflections (All) 1 1.4 1.48 84.7 0.6 0.6 1.3 4.4 6914
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS STRUCTURE SOLVED INITIALLY IN SAME CRYSTAL FORM SOAKED WITH SODIUM IODIDE AND SAD PHASED 1.4 30.728 53419 53419 2726 93.22 0.1547 0.1547 0.1529 0.1554 0.1886 0.1886 RANDOM 16.6572
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 Key Refinement Restraint Deviation f_dihedral_angle_d 15.913 f_angle_d 1.232 f_chiral_restr 0.061 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2451 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms 22
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction PHENIX phasing