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Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the expression tag bound in the substrate binding site of a neighbouring molecule at 2.37 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 2.68 54.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.268 α = 90 b = 78.418 β = 93.1 c = 106.465 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) Rpim 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 2.37 42.486 94.9 0.233 0.233 0.964 2.6 2.1 43453
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.37 2.46 97.4 1.235 1.234 0.34 0.8 2.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.37 42.486 43453 863 94.377 0.22 0.2197 0.2464 0.253 44.031
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] 1.857 0.133 0.74 -2.596
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.875 r_dihedral_angle_6_deg 14.499 r_dihedral_angle_3_deg 13.527 r_lrange_other 11.447 r_lrange_it 11.445 r_dihedral_angle_1_deg 5.956 r_scangle_it 5.855 r_scangle_other 5.854 r_mcangle_it 5.355 r_mcangle_other 5.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.875 r_dihedral_angle_6_deg 14.499 r_dihedral_angle_3_deg 13.527 r_lrange_other 11.447 r_lrange_it 11.445 r_dihedral_angle_1_deg 5.956 r_scangle_it 5.855 r_scangle_other 5.854 r_mcangle_it 5.355 r_mcangle_other 5.355 r_scbond_it 3.444 r_scbond_other 3.444 r_mcbond_it 3.207 r_mcbond_other 3.207 r_angle_refined_deg 1.317 r_angle_other_deg 0.72 r_nbd_other 0.245 r_symmetry_xyhbond_nbd_refined 0.23 r_symmetry_nbd_other 0.209 r_nbd_refined 0.198 r_symmetry_nbd_refined 0.194 r_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.173 r_ncsr_local_group_10 0.146 r_ncsr_local_group_2 0.139 r_ncsr_local_group_11 0.138 r_ncsr_local_group_6 0.131 r_ncsr_local_group_12 0.131 r_ncsr_local_group_13 0.128 r_ncsr_local_group_3 0.116 r_ncsr_local_group_15 0.116 r_ncsr_local_group_8 0.114 r_ncsr_local_group_7 0.107 r_ncsr_local_group_14 0.107 r_ncsr_local_group_1 0.106 r_ncsr_local_group_5 0.106 r_ncsr_local_group_9 0.09 r_ncsr_local_group_4 0.087 r_symmetry_nbtor_other 0.082 r_xyhbond_nbd_other 0.069 r_chiral_restr 0.064 r_symmetry_xyhbond_nbd_other 0.053 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7662 Nucleic Acid Atoms Solvent Atoms 573 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction autoPROC data scaling MOLREP phasing Coot model building