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Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter sp. with the expression tag bound in the substrate binding site of a neighbouring molecule at 2.41 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8I8I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 BIS-TRIS propane pH 7.0, Sodium citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 2.71 54.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.692 α = 90 b = 78.682 β = 93.077 c = 106.902 γ = 90
Symmetry Space Group C 1 2 1
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 PILATUS3 2M 2022-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.41 106.75 94.4 0.194 0.975 4.8 2.2 41591 36
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.41 2.5 87.4 1.019 0.391 1.1 2.2
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 2.41 106.748 41591 2078 93.804 0.211 0.2086 0.2135 0.2627 0.2646 46.791
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] 1.303 0.11 1.58 -2.879
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.405 r_dihedral_angle_3_deg 13.347 r_lrange_other 10.297 r_lrange_it 10.295 r_dihedral_angle_2_deg 9.371 r_dihedral_angle_1_deg 6.701 r_scangle_it 6.316 r_scangle_other 6.315 r_mcangle_it 5.857 r_mcangle_other 5.857
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.405 r_dihedral_angle_3_deg 13.347 r_lrange_other 10.297 r_lrange_it 10.295 r_dihedral_angle_2_deg 9.371 r_dihedral_angle_1_deg 6.701 r_scangle_it 6.316 r_scangle_other 6.315 r_mcangle_it 5.857 r_mcangle_other 5.857 r_scbond_it 3.722 r_scbond_other 3.722 r_mcbond_it 3.528 r_mcbond_other 3.528 r_angle_refined_deg 1.375 r_angle_other_deg 0.739 r_nbd_other 0.241 r_symmetry_nbd_other 0.212 r_nbd_refined 0.208 r_symmetry_nbd_refined 0.202 r_symmetry_xyhbond_nbd_refined 0.195 r_xyhbond_nbd_refined 0.192 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_other 0.086 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.061 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7662 Nucleic Acid Atoms Solvent Atoms 519 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction Aimless data scaling MOLREP phasing Coot model building