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Crystal structure of Phosphopantetheine adenylyltransferase from Klebsiella pneumoniae at 2.59 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B6T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1M HEPES pH 7.5, 20% PEG 10000
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.819 α = 90 b = 72.819 β = 90 c = 200.365 γ = 90
Symmetry Space Group P 41 21 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 6M 2021-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87 ESRF ID23-2
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 2.59 41.27 99.7 0.998 3.21 4 17572 48.8
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 2.59 2.67 0.88
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 2.59 41.27 17572 632 99.949 0.21 0.2079 0.2124 0.2549 0.2525 55.056
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] -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.267 r_dihedral_angle_3_deg 15.562 r_lrange_other 11.15 r_lrange_it 11.133 r_scangle_it 7.42 r_scangle_other 7.419 r_mcangle_it 6.965 r_mcangle_other 6.964 r_dihedral_angle_1_deg 5.82 r_scbond_it 4.552
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.267 r_dihedral_angle_3_deg 15.562 r_lrange_other 11.15 r_lrange_it 11.133 r_scangle_it 7.42 r_scangle_other 7.419 r_mcangle_it 6.965 r_mcangle_other 6.964 r_dihedral_angle_1_deg 5.82 r_scbond_it 4.552 r_scbond_other 4.551 r_mcbond_it 4.311 r_mcbond_other 4.309 r_dihedral_angle_2_deg 3.472 r_angle_refined_deg 1.179 r_angle_other_deg 0.395 r_nbd_other 0.29 r_symmetry_nbd_refined 0.237 r_symmetry_nbd_other 0.218 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.198 r_symmetry_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.171 r_symmetry_nbtor_other 0.077 r_symmetry_xyhbond_nbd_other 0.056 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3720 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing