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Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared crystal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IWB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 293 10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6
Crystal Properties Matthews coefficient Solvent content 1.98 37.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.687 α = 80.78 b = 95.459 β = 87.58 c = 114.567 γ = 81.1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2017-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0000 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.7 47 94.2 0.058 0.082 0.997 8.33 1.8 313887
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 90.3 0.648 0.917 0.539 1.06 1.8
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 1IWB 1.7 47 1.96 302964 3094 91.03 0.1498 0.1495 0.1496 0.1867 0.1864
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 13.477 f_angle_d 1.096 f_chiral_restr 0.055 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26686 Nucleic Acid Atoms Solvent Atoms 2950 Heterogen Atoms 460
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing