☰ Navigation Tabs
RibB from Vibrio cholera bound with L-xylulose-5-phosphate (L-Xy5P) and manganese
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P8E PDB entry 4P8E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1 M lithium acetate, 12-18% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.31 46.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.369 α = 90 b = 79.016 β = 90 c = 91.349 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 2019-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2 39.51 99.6 0.043 16.9 6.6 15092 23.26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 0.256 3.8
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 PDB entry 4P8E 2 39.51 1.33 15068 1507 99.72 0.1665 0.1612 0.1677 0.2136 0.2198 26.69
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 15.828 f_angle_d 1.1167 f_chiral_restr 0.0548 f_bond_d 0.0108 f_plane_restr 0.0077
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1631 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing