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Crystal Structure of the type II Dehydroquinate dehydratase from Acinetobacter baumannii at 2.03A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LWZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 30% PEG3350, MgSO4, Tris buffer, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.6 52.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.284 α = 90 b = 95.279 β = 95.73 c = 132.263 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MARRESEARCH mirror 2014-04-08 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 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 2.03 50 97.3 0.09 31 124546
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 2.03 2.07 100 0.441 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 3LWZ 2.05 47 116575 6049 96.17 0.19321 0.1905 0.2046 0.24488 0.2467 RANDOM 32.311
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] 0.63 -0.08 0.07 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.647 r_dihedral_angle_3_deg 15.885 r_dihedral_angle_4_deg 12.236 r_long_range_B_refined 8.913 r_long_range_B_other 8.879 r_dihedral_angle_1_deg 6.984 r_scangle_other 5.732 r_mcangle_other 5.665 r_mcangle_it 5.663 r_scbond_it 3.667
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.647 r_dihedral_angle_3_deg 15.885 r_dihedral_angle_4_deg 12.236 r_long_range_B_refined 8.913 r_long_range_B_other 8.879 r_dihedral_angle_1_deg 6.984 r_scangle_other 5.732 r_mcangle_other 5.665 r_mcangle_it 5.663 r_scbond_it 3.667 r_scbond_other 3.617 r_mcbond_it 3.495 r_mcbond_other 3.487 r_angle_refined_deg 1.87 r_angle_other_deg 0.948 r_chiral_restr 0.128 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 13968 Nucleic Acid Atoms Solvent Atoms 769 Heterogen Atoms 60
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling