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Crystal structure of dehydroquinate dehydratase with tris induced oligomerisation at 1.907 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B6P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 1.5M Ammonium sulphate, 0.1M tris, 12% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.6 52.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.904 α = 90 b = 155.606 β = 90 c = 155.912 γ = 90
Symmetry Space Group P 21 21 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 PILATUS3 S 6M 2017-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97 ESRF ID29
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 1.91 45.7 89.8 0.134 5.96 3.2 139447
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.91 1.956
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 5B6P 1.91 45.7 137982 1465 89.75 0.20044 0.19992 0.208 0.24779 0.2545 RANDOM 45.754
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] 0.71 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.595 r_dihedral_angle_3_deg 16.447 r_dihedral_angle_4_deg 13.924 r_long_range_B_refined 10.356 r_long_range_B_other 10.353 r_dihedral_angle_1_deg 6.48 r_scangle_other 6.43 r_mcangle_it 5.769 r_mcangle_other 5.769 r_scbond_it 4.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.595 r_dihedral_angle_3_deg 16.447 r_dihedral_angle_4_deg 13.924 r_long_range_B_refined 10.356 r_long_range_B_other 10.353 r_dihedral_angle_1_deg 6.48 r_scangle_other 6.43 r_mcangle_it 5.769 r_mcangle_other 5.769 r_scbond_it 4.112 r_scbond_other 4.111 r_mcbond_it 3.702 r_mcbond_other 3.701 r_angle_refined_deg 1.687 r_angle_other_deg 1.048 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13466 Nucleic Acid Atoms Solvent Atoms 506 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data processing Coot model building MOLREP phasing XDS data reduction SCALEPACK data scaling