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Crystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Dephospho Coenzyme A at 2.90A 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 5.6 298 1M LITHIUM SULPHATE, 0.5M AMMONIUM SULPHATE, 0.1M SODIUM CITRATE, PH- 5.6
Crystal Properties Matthews coefficient Solvent content 5.6 78.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 216.479 α = 90 b = 216.479 β = 90 c = 216.479 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 2018-05-14 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 2.9 48.41 99.9 0.105 0.99 26.7 20 9622
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.97 99.7 0.99 0.76 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 2.9 44.19 9622 507 99.91 0.18023 0.17685 0.1802 0.24138 0.24 RANDOM 70
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 33.995 r_dihedral_angle_3_deg 24.034 r_long_range_B_other 20.985 r_long_range_B_refined 20.947 r_dihedral_angle_4_deg 20.495 r_scangle_other 16.971 r_mcangle_it 12.926 r_mcangle_other 12.92 r_scbond_it 11.651 r_scbond_other 11.648
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.995 r_dihedral_angle_3_deg 24.034 r_long_range_B_other 20.985 r_long_range_B_refined 20.947 r_dihedral_angle_4_deg 20.495 r_scangle_other 16.971 r_mcangle_it 12.926 r_mcangle_other 12.92 r_scbond_it 11.651 r_scbond_other 11.648 r_mcbond_it 9.124 r_mcbond_other 9.12 r_dihedral_angle_1_deg 7.103 r_angle_refined_deg 1.878 r_angle_other_deg 1.053 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 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 23 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling MOLREP phasing