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Vibrio cholerae Oligoribonuclease bound to pAA
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 3.18 61.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.375 α = 90 b = 89.375 β = 90 c = 59.451 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 2018-03-22 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 1.619 47.148 99.9 0.047 0.049 0.014 28.1 12 35203 26.32
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 1.62 1.71 99.3 1.06 1.06 1.11 0.326 0.7 11.3
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 1.619 24.75 1.34 35163 1762 99.88 0.1466 0.1461 0.1483 0.1546 0.1567 32.5809
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 7.566 f_angle_d 0.816 f_chiral_restr 0.054 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 45 Solvent Atoms 268 Heterogen Atoms 1
Software Software Software Name Purpose XDS data reduction SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction PHENIX phasing