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Glycerol bound structure of Obc1, a bifunctional enzyme for quorum sensing-dependent oxalogenesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IKY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 0.1M HEPES pH 7.0, 1M Sodium citrate tribasic
Crystal Properties Matthews coefficient Solvent content 5.23 76.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 229.97 α = 90 b = 229.97 β = 90 c = 253.763 γ = 120
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 ADSC QUANTUM 270 2012-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.9793 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.8 78.34 100 0.277 0.996 12.4 19.6 63296 56.96
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 100 2.647 17.5
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 5IKY 2.8 46.349 1.34 63263 3166 99.95 0.2 0.1985 0.2052 0.2274 0.2332 69.4751
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 12.101 f_angle_d 0.69 f_chiral_restr 0.026 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7848 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 7
Software Software Software Name Purpose MOSFLM data collection Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHENIX phasing