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Crystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Pyrophosphate at 2.30A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZZC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 1M LITHIUM SULPHATE, 0.5M AMMONIUM SULPHATE, 0.1M SODIUM CITRATE, PH 5.6
Crystal Properties Matthews coefficient Solvent content 5.6 78.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 216.12 α = 90 b = 216.12 β = 90 c = 216.12 γ = 90
Symmetry Space Group F 41 3 2
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 PILATUS 2M mirror 2018-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97199 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.3 76.41 100 0.16 0.16 16.6 20 19784
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 2.3 2.38 100 0.8 5.3
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 5ZZC 2.3 76.41 18770 1010 99.99 0.1875 0.18569 0.1907 0.21914 0.2266 RANDOM 47.693
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.085 r_dihedral_angle_4_deg 22.409 r_dihedral_angle_3_deg 20.675 r_long_range_B_other 13.987 r_long_range_B_refined 13.963 r_scangle_other 11.198 r_mcangle_it 8.116 r_mcangle_other 8.115 r_scbond_it 7.788 r_scbond_other 7.554
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.085 r_dihedral_angle_4_deg 22.409 r_dihedral_angle_3_deg 20.675 r_long_range_B_other 13.987 r_long_range_B_refined 13.963 r_scangle_other 11.198 r_mcangle_it 8.116 r_mcangle_other 8.115 r_scbond_it 7.788 r_scbond_other 7.554 r_dihedral_angle_1_deg 7.065 r_mcbond_it 5.547 r_mcbond_other 5.467 r_angle_refined_deg 2.103 r_angle_other_deg 1.442 r_chiral_restr 0.091 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.001 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 1305 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing