☰ Navigation Tabs
Crystal structure a Thioredoxin Reductase from Gloeobacter violaceus bound to its electron donor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J60
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 40% PEG-300
100 mM Sodium cacodylate-HCl, pH 6.5
200 mM Sodium acetate
Crystal Properties Matthews coefficient Solvent content 3.43 64.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.741 α = 90 b = 181.312 β = 90 c = 80.369 γ = 90
Symmetry Space Group C 2 2 21
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-F 2019-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91589 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.23 83.4 92.7 0.298 0.31 0.085 0.989 9.3 13.1 40062 27.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.23 2.47 64.5 1.673 1.763 0.549 0.584 1.6 10.2
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 5J60 2.23 83.37 1.34 40054 2035 66.99 0.2021 0.2005 0.2001 0.2315 0.2285 37.21
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 19.0558 f_angle_d 1.1728 f_chiral_restr 0.0653 f_bond_d 0.0068 f_plane_restr 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6156 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 308
Software Software Software Name Purpose PHENIX refinement XDS data reduction autoPROC data scaling PHASER phasing