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Crystal structure of apo-form of dehydroquinate dehydratase from Corynebacterium glutamicum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V1J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 PEG 3350, Ammonium citrate tribasic
Crystal Properties Matthews coefficient Solvent content 2.28 46.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.531 α = 90 b = 81.531 β = 90 c = 221.807 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 CCD ADSC QUANTUM 270 2022-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 50 99 0.065 17.9 2.7 47482
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 99 0.274 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 26.51 47482 2494 97.95 0.16006 0.15778 0.1611 0.20279 0.2043 RANDOM 24.309
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] 0.4 0.2 0.4 -1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.705 r_dihedral_angle_4_deg 15.071 r_dihedral_angle_3_deg 12.979 r_dihedral_angle_1_deg 6.591 r_long_range_B_refined 6.018 r_long_range_B_other 5.885 r_scangle_other 4.249 r_scbond_it 2.939 r_scbond_other 2.936 r_mcangle_other 2.817
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.705 r_dihedral_angle_4_deg 15.071 r_dihedral_angle_3_deg 12.979 r_dihedral_angle_1_deg 6.591 r_long_range_B_refined 6.018 r_long_range_B_other 5.885 r_scangle_other 4.249 r_scbond_it 2.939 r_scbond_other 2.936 r_mcangle_other 2.817 r_mcangle_it 2.813 r_mcbond_it 1.977 r_mcbond_other 1.959 r_angle_refined_deg 1.587 r_angle_other_deg 1.447 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 4369 Nucleic Acid Atoms Solvent Atoms 589 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing