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Crystal structure of dodecameric Dehydroquinate dehydratase from Acinetobacter baumannii at 1.9A 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 Sulfate, 0.1M tris pH 8.5, 12% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.54 51.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.796 α = 90 b = 155.129 β = 90 c = 155.465 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 CCD MARRESEARCH 2017-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.972 ESRF ID29
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 1.9 49.15 93 0.096 9.3 4.4 146433
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 1.9 1.945 94.6 0.756 4.2
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 5B6P 1.9 49.15 144895 1538 93.36 0.18177 0.18141 0.1914 0.21764 0.2214 RANDOM 47.053
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] -0.35 0.1 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.517 r_dihedral_angle_3_deg 17.694 r_dihedral_angle_4_deg 13.11 r_long_range_B_refined 10.561 r_long_range_B_other 10.561 r_scangle_other 7.309 r_dihedral_angle_1_deg 6.078 r_mcangle_it 5.416 r_mcangle_other 5.415 r_scbond_it 4.811
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.517 r_dihedral_angle_3_deg 17.694 r_dihedral_angle_4_deg 13.11 r_long_range_B_refined 10.561 r_long_range_B_other 10.561 r_scangle_other 7.309 r_dihedral_angle_1_deg 6.078 r_mcangle_it 5.416 r_mcangle_other 5.415 r_scbond_it 4.811 r_scbond_other 4.811 r_mcbond_it 3.57 r_mcbond_other 3.569 r_angle_other_deg 2.509 r_angle_refined_deg 2.058 r_chiral_restr 0.132 r_bond_refined_d 0.023 r_bond_other_d 0.018 r_gen_planes_refined 0.015 r_gen_planes_other 0.011 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 575 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling MOLREP phasing