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The crystal structure of type II Dehydroquinase from Butyrivibrio crossotus DSM 2876
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HS9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 20% PEG 4000, 0.2M Ammonium sulfate, 0.1M sodium citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.67 53.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.476 α = 90 b = 79.476 β = 90 c = 72.033 γ = 120
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 PILATUS3 S 6M 2016-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.826560 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 0.92 31.93 96.7 0.046 0.055 0.03 0.997 14.1 3.2 112975 6.6
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 0.923 0.939 85.9 0.331 0.426 0.265 0.762 2.6 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6HS9 0.92 31.93 107213 5762 96.73 0.1022 0.1013 0.1293 0.1198 0.1421 RANDOM 12.663
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] -0.08 -0.04 -0.08 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.466 r_sphericity_free 28.099 r_dihedral_angle_4_deg 14.446 r_dihedral_angle_3_deg 12.557 r_sphericity_bonded 9.325 r_dihedral_angle_1_deg 6.137 r_rigid_bond_restr 3.712 r_angle_refined_deg 2.04 r_angle_other_deg 0.729 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.466 r_sphericity_free 28.099 r_dihedral_angle_4_deg 14.446 r_dihedral_angle_3_deg 12.557 r_sphericity_bonded 9.325 r_dihedral_angle_1_deg 6.137 r_rigid_bond_restr 3.712 r_angle_refined_deg 2.04 r_angle_other_deg 0.729 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1150 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing