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Structure of the dodecameric type-II dehydrogenate dehydratase from Acinetobacter baumannii at 2.00 A 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% PEG 3350, MgSO4, Tris buffer, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.6 53
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 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 2 131.6 96.2 0.09 31 7.6 129427 22.8
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 2.03 100 0.441 4.6 7.7
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 2 131.6 129427 1588 96.2 0.20098 0.20059 0.2084 0.23215 0.2382 RANDOM 29.142
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 -0.09 0.09 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.781 r_dihedral_angle_3_deg 14.775 r_dihedral_angle_4_deg 11.453 r_long_range_B_refined 7.812 r_long_range_B_other 7.811 r_dihedral_angle_1_deg 6.262 r_scangle_other 5.547 r_mcangle_it 4.625 r_mcangle_other 4.625 r_scbond_it 3.563
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.781 r_dihedral_angle_3_deg 14.775 r_dihedral_angle_4_deg 11.453 r_long_range_B_refined 7.812 r_long_range_B_other 7.811 r_dihedral_angle_1_deg 6.262 r_scangle_other 5.547 r_mcangle_it 4.625 r_mcangle_other 4.625 r_scbond_it 3.563 r_scbond_other 3.56 r_mcbond_it 3.052 r_mcbond_other 3.047 r_angle_other_deg 2.482 r_angle_refined_deg 1.909 r_chiral_restr 0.157 r_bond_refined_d 0.02 r_bond_other_d 0.016 r_gen_planes_refined 0.013 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 13452 Nucleic Acid Atoms Solvent Atoms 769 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing