☰ Navigation Tabs
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, SITTING DROP 7.5 293 10% PEG 8000, 0.1M CaCl2, 0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.69 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.55 α = 90 b = 79.55 β = 90 c = 72.28 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) 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 1.05 32.04 99.5 0.054 0.047 0.028 0.998 13.9 4.8 119959 12.298
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 1.05 1.07 98.8 0.717 0.914 0.559 0.477 1.4 2.4
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 1.05 32 74983 4062 99.26 0.1139 0.1128 0.1146 0.134 0.1355 RANDOM 21.112
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] -0.21 -0.1 -0.21 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.998 r_dihedral_angle_4_deg 26.117 r_sphericity_free 24.668 r_dihedral_angle_3_deg 13.488 r_sphericity_bonded 12.956 r_dihedral_angle_1_deg 5.862 r_rigid_bond_restr 5.076 r_angle_refined_deg 2.051 r_angle_other_deg 0.712 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.998 r_dihedral_angle_4_deg 26.117 r_sphericity_free 24.668 r_dihedral_angle_3_deg 13.488 r_sphericity_bonded 12.956 r_dihedral_angle_1_deg 5.862 r_rigid_bond_restr 5.076 r_angle_refined_deg 2.051 r_angle_other_deg 0.712 r_chiral_restr 0.129 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1150 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 19
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction