☰ Navigation Tabs
Crystal structure of the bacterial oxalate transporter OxlT in a ligand-free outward-facing form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8HPK OxlT experimental model PDB 5B3N scFv fragment
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 9 293 100 mM Glycine, pH 9.0, 26-36% (v/v) PEG 400, 50-150 mM MnCl2
Crystal Properties Matthews coefficient Solvent content 3.72 66.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.87 α = 90 b = 181.67 β = 111.365 c = 81.17 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2015-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 3.1 47.26 88.4 0.98 5 24.8 26204 52.81
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.4 0.69
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 8HPK, 5B3N 3.3 47.26 1.34 25428 1265 81.6 0.261 0.2596 0.2599 0.2859 0.2839 53.88
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 17.5072 f_angle_d 0.5938 f_chiral_restr 0.0404 f_plane_restr 0.0061 f_bond_d 0.0025
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9517 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose Coot model building PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing