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Crystal structure of 3-deoxy-8-phosphooctulonate synthase from Acinetobacter baumannii
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 200 mM Lithium sulfate, 10% (w/v) PEG 3000, 100 mM Imidazole/ Hydrochloric acid pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.42 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.582 α = 90 b = 89.119 β = 114.98 c = 92.677 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 100 PIXEL DECTRIS EIGER X 16M 2025-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97918 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.59 34.13 100 0.993 8.2 6.7 161001
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.63 0.655
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 1.71 33.7 123107 6547 99.76 0.17832 0.17669 0.1886 0.20895 0.2175 RANDOM 18.312
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] -0.49 0.11 -0.51 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.994 r_dihedral_angle_2_deg 9.761 r_dihedral_angle_1_deg 6.457 r_long_range_B_refined 5.888 r_long_range_B_other 5.785 r_scangle_other 4.689 r_scbond_other 2.947 r_scbond_it 2.946 r_mcangle_it 2.785 r_mcangle_other 2.785
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.994 r_dihedral_angle_2_deg 9.761 r_dihedral_angle_1_deg 6.457 r_long_range_B_refined 5.888 r_long_range_B_other 5.785 r_scangle_other 4.689 r_scbond_other 2.947 r_scbond_it 2.946 r_mcangle_it 2.785 r_mcangle_other 2.785 r_mcbond_it 1.846 r_mcbond_other 1.846 r_angle_refined_deg 1.752 r_angle_other_deg 0.599 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 8690 Nucleic Acid Atoms Solvent Atoms 841 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DIALS data scaling xia2 data reduction PHENIX phasing PDB_EXTRACT data extraction