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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 1GQO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 10% MPD, 0.1M Sodium tartrate, 0.1M Sodium Acetate
Crystal Properties Matthews coefficient Solvent content 2.51 51.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.33 α = 90 b = 125.33 β = 90 c = 125.33 γ = 90
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-F 2018-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.915870 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.7 37.79 99.8 0.054 0.06 0.025 0.999 18.3 5.7 17966 27.7
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 1.7 1.73 99.89 1.518 1.677 0.702 0.554 1.4 5.5
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 1GQO 1.7 37.79 17098 854 99.61 0.1433 0.1416 0.1555 0.1793 0.1818 RANDOM 31.16
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 r_dihedral_angle_2_deg 35.264 r_dihedral_angle_4_deg 19.98 r_dihedral_angle_3_deg 13.034 r_dihedral_angle_1_deg 6.498 r_angle_refined_deg 1.659 r_angle_other_deg 1.008 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.264 r_dihedral_angle_4_deg 19.98 r_dihedral_angle_3_deg 13.034 r_dihedral_angle_1_deg 6.498 r_angle_refined_deg 1.659 r_angle_other_deg 1.008 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1145 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 41
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction