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Crystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Dephospho Coenzyme A at 2.75 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YH7
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 5.75 78.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 216.883 α = 90 b = 216.883 β = 90 c = 216.883 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 EIGER X 9M mirror 2018-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9677 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.75 48.5 99.8 0.14 0.99 15.04 20 11866 63.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.82 100 0.47 0.98 8.05 15
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 5yh7 2.75 48.5 11271 594 99.76 0.18323 0.18097 0.1902 0.2268 0.233 RANDOM 56.885
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 28.666 r_dihedral_angle_3_deg 20.252 r_dihedral_angle_4_deg 19.51 r_long_range_B_refined 13.292 r_long_range_B_other 13.226 r_scangle_other 10.518 r_mcangle_it 9.048 r_mcangle_other 9.043 r_scbond_it 7.13 r_dihedral_angle_1_deg 7.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.666 r_dihedral_angle_3_deg 20.252 r_dihedral_angle_4_deg 19.51 r_long_range_B_refined 13.292 r_long_range_B_other 13.226 r_scangle_other 10.518 r_mcangle_it 9.048 r_mcangle_other 9.043 r_scbond_it 7.13 r_dihedral_angle_1_deg 7.125 r_scbond_other 7.082 r_mcbond_it 5.965 r_mcbond_other 5.965 r_angle_refined_deg 1.941 r_angle_other_deg 1.012 r_chiral_restr 0.078 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 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 41 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling MOLREP phasing