☰ Navigation Tabs
Crystal structure of a TRAP periplasmic solute binding protein from Fusobacterium nucleatun (FN1258, TARGET EFI-510120) with bound SN-glycerol-3-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N6K PDB entry 4N6K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 Protein (70.0 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM Glycerol 3-phosphate); Reservoir (0.2 M Zinc Acetate, 0.1 M Imidazole pH 6.5, 10 %(w/v) PEG 8000); Cryoprotection (80% Reservoir + 20% Glycerol
Crystal Properties Matthews coefficient Solvent content 3.25 62.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.574 α = 90 b = 113.574 β = 90 c = 79.937 γ = 90
Symmetry Space Group P 43 2 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 2013-12-06 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 Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.7 113.574 99.9 0.166 0.173 0.05 10.4 11.8 14902 14902 52.93
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.85 100 0.854 0.854 0.254 0.9 12 2135
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 4N6K 2.7 40.154 1.36 14870 753 99.77 0.1663 0.1644 0.1699 0.2037 0.203 Random Selection 40.85
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 15.4 f_angle_d 1.094 f_chiral_restr 0.072 f_bond_d 0.012 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2419 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 25
Software Software Software Name Purpose SCALA data scaling PDB_EXTRACT data extraction PHENIX refinement SCALA data scaling