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Crystal Structure of the Succinyl-diaminopimelate Desuccinylase (DapE) from Acinetobacter baumannii in complex with Succinic and L-Lactic Acids
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7T1Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 292 Protein: 8.0 mg/ml, 0.15M Sodium chloride, 0.01M Tris pH 8.3, 2mM N6-Me-L,L-SDAP;
Screen: Peg's II (H1), 0.1M M tri-Sodium citrate, 33% (w/v) PEG6000.
Crystal Properties Matthews coefficient Solvent content 2.92 57.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.659 α = 90 b = 102.533 β = 90 c = 145.491 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 PIXEL DECTRIS EIGER X 9M 2021-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97864 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.1 30 99.7 0.143 0.143 0.154 0.056 0.994 12.6 7.4 59464 -3 37.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 99.9 0.419 0.492 1.8 7.7
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 2.1 29.86 56580 3030 99.59 0.19116 0.18901 0.1978 0.22965 0.2396 RANDOM 48.327
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] 7.22 -2.33 -4.89
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 8.191 r_long_range_B_refined 8.156 r_dihedral_angle_3_deg 6.914 r_scangle_other 5.434 r_mcangle_it 4.237 r_mcangle_other 4.236 r_scbond_it 3.814 r_scbond_other 3.773 r_mcbond_it 2.967 r_mcbond_other 2.967
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 8.191 r_long_range_B_refined 8.156 r_dihedral_angle_3_deg 6.914 r_scangle_other 5.434 r_mcangle_it 4.237 r_mcangle_other 4.236 r_scbond_it 3.814 r_scbond_other 3.773 r_mcbond_it 2.967 r_mcbond_other 2.967 r_dihedral_angle_1_deg 2.902 r_dihedral_angle_2_deg 2.245 r_angle_refined_deg 1.325 r_angle_other_deg 0.548 r_chiral_restr 0.064 r_gen_planes_refined 0.022 r_gen_planes_other 0.02 r_bond_other_d 0.014 r_bond_refined_d 0.005 r_dihedral_angle_4_deg 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 5753 Nucleic Acid Atoms Solvent Atoms 378 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing