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Crystal structure of the complex of phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Dephosphocoenzyme-A at 2.19 A 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, 2M AMMONIUM SULPHATE, 0.1M SODIUM CITRATE, PH 5.6
Crystal Properties Matthews coefficient Solvent content 5.76 78.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 217.038 α = 90 b = 217.038 β = 90 c = 217.038 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 PSI PILATUS 6M 2018-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97199 ESRF ID23-1
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 2.19 125.307 95.48 0.99 16.2 20 22090
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 2.19 2.25 0.631
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.19 125.307 22090 1044 95.582 0.203 0.2011 0.2113 0.2367 0.2414 63.419
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_6_deg 18.635 r_dihedral_angle_3_deg 17.17 r_lrange_it 15.806 r_lrange_other 15.652 r_scangle_it 13.612 r_scangle_other 13.611 r_dihedral_angle_2_deg 13.226 r_scbond_it 9.399 r_scbond_other 9.337 r_mcangle_other 8.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.635 r_dihedral_angle_3_deg 17.17 r_lrange_it 15.806 r_lrange_other 15.652 r_scangle_it 13.612 r_scangle_other 13.611 r_dihedral_angle_2_deg 13.226 r_scbond_it 9.399 r_scbond_other 9.337 r_mcangle_other 8.802 r_mcangle_it 8.764 r_dihedral_angle_1_deg 7.381 r_mcbond_it 6.455 r_mcbond_other 6.449 r_angle_refined_deg 2.068 r_dihedral_angle_other_2_deg 1.34 r_angle_other_deg 1.105 r_nbd_other 0.296 r_symmetry_nbd_refined 0.295 r_xyhbond_nbd_refined 0.292 r_symmetry_nbd_other 0.224 r_nbd_refined 0.222 r_symmetry_xyhbond_nbd_refined 0.198 r_metal_ion_refined 0.196 r_nbtor_refined 0.195 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.092 r_symmetry_xyhbond_nbd_other 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.008 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1305 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing