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Crystal structure of dehydroquinate dehydratase from Acinetobacter baumannii at 2.5 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WRF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 30% PEG3350, MgSO4, Tris buffer
Crystal Properties Matthews coefficient Solvent content 2.49 50.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.993 α = 90 b = 136.254 β = 97.59 c = 143.209 γ = 90
Symmetry Space Group C 1 2 1
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 MARRESEARCH 2016-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.54 49.15 69.4 0.168 7.18 2.55 61621
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.54 2.59 92 0.383 1.3 1.2
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 5WRF 2.54 47.932 41209 2142 70.32 0.25521 0.2526 0.2576 0.30524 0.3072 RANDOM 51.292
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] 2.65 -1.17 -5.55 3.1
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 78.165 r_dihedral_angle_2_deg 37.332 r_dihedral_angle_3_deg 22.112 r_sphericity_bonded 20.978 r_dihedral_angle_4_deg 20.258 r_rigid_bond_restr 16.51 r_long_range_B_refined 8.706 r_long_range_B_other 8.68 r_scangle_other 7.504 r_mcangle_it 6.706
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 78.165 r_dihedral_angle_2_deg 37.332 r_dihedral_angle_3_deg 22.112 r_sphericity_bonded 20.978 r_dihedral_angle_4_deg 20.258 r_rigid_bond_restr 16.51 r_long_range_B_refined 8.706 r_long_range_B_other 8.68 r_scangle_other 7.504 r_mcangle_it 6.706 r_mcangle_other 6.706 r_scbond_it 5.817 r_scbond_other 5.817 r_dihedral_angle_1_deg 5.091 r_mcbond_it 5.042 r_mcbond_other 5.042 r_angle_other_deg 4.835 r_angle_refined_deg 2.12 r_chiral_restr 0.147 r_bond_other_d 0.048 r_gen_planes_other 0.028 r_bond_refined_d 0.025 r_gen_planes_refined 0.023 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13440 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing