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Structure of a novel oxidoreductase from Gloeobacter violaceus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JRI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 1.5 M Li2SO4
0.1 M HEPES, pH 7.5
Crystals were soaked for 5 min in a solution of mother liquor plus 0.1 M reduced Glutathione, immersed in a solution of mother liquor containing 25% Ethylene glycol and immediately flash-frozen in liquid nitrogen
Crystal Properties Matthews coefficient Solvent content 3.54 65.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.842 α = 90 b = 143.325 β = 90 c = 265.111 γ = 90
Symmetry Space Group I 2 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 PIXEL DECTRIS PILATUS 6M 2016-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.99989 ALBA XALOC
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 1.949 49.73 99.03 0.17 0.997 9.19 10 80406
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.949 2.019 95.71 2.84 0.472 0.88 10
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 5JRI 1.949 49.728 1.33 80159 3961 98.98 0.2033 0.2017 0.2136 0.2336 0.2441
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 13.971 f_angle_d 1.105 f_chiral_restr 0.061 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4679 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 287
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing