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E.coli DsbB C104S with ubiquinone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B3P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 295 34% PEG 400, 60 mM NaCl, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.54 51.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.381 α = 90 b = 53.381 β = 90 c = 280.74 γ = 120
Symmetry Space Group P 32 2 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 PILATUS 6M-F 2019-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
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 2.68 46.23 97.6 0.185 0.203 0.082 0.998 9.1 5.8 13571
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 2.68 2.81 88.5 7.897 8.684 3.507 0.262 5.6
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 THROUGHOUT 2B3P 2.9 46.23 1.33 10859 504 97.76 0.26 0.2588 0.2649 0.2862 0.3035 113.0847
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 20.459 f_angle_d 0.501 f_chiral_restr 0.04 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3088 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 18
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing