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Vibrio cholerae Oligoribonuclease bound to pGA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6N6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.1 M BisTris (pH 5.5), 17% polyethylene glycol 3350, and 20% xylitol
Crystal Properties Matthews coefficient Solvent content 3.21 61.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.615 α = 90 b = 89.615 β = 90 c = 59.683 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 2018-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.977 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.578 47.311 99.8 0.06 0.064 0.022 17.8 8.4 38266 38266 22.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.66 98.7 0.938 0.938 1 0.34 0.8 8.3
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 6N6A 1.578 47.311 1.34 38236 1916 99.74 0.1524 0.152 0.1543 0.1588 0.1612 29.4033
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 7.562 f_angle_d 0.808 f_chiral_restr 0.055 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1469 Nucleic Acid Atoms 46 Solvent Atoms 266 Heterogen Atoms 1
Software Software Software Name Purpose XDS data reduction SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction PHENIX phasing