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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 2.25 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 54.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.925 α = 90 b = 78.622 β = 93.118 c = 106.985 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 2.25 42.668 96.3 0.134 0.133 0.98 4.6 2.1 52114
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 2.25 2.32 0.722 0.721 0.445 1.3
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 2.25 42.668 52073 1057 95.745 0.226 0.225 0.2301 0.2513 0.2559 42.291
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] 1.301 0.507 1.116 -2.458
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.214 r_dihedral_angle_3_deg 13.215 r_lrange_other 11.561 r_lrange_it 11.56 r_dihedral_angle_2_deg 8.784 r_scangle_it 6.846 r_scangle_other 6.846 r_dihedral_angle_1_deg 5.879 r_mcangle_it 5.8 r_mcangle_other 5.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.214 r_dihedral_angle_3_deg 13.215 r_lrange_other 11.561 r_lrange_it 11.56 r_dihedral_angle_2_deg 8.784 r_scangle_it 6.846 r_scangle_other 6.846 r_dihedral_angle_1_deg 5.879 r_mcangle_it 5.8 r_mcangle_other 5.8 r_scbond_it 4.269 r_scbond_other 4.269 r_mcbond_it 3.688 r_mcbond_other 3.688 r_angle_refined_deg 1.382 r_angle_other_deg 0.747 r_nbd_other 0.3 r_symmetry_xyhbond_nbd_refined 0.243 r_symmetry_nbd_refined 0.221 r_symmetry_nbd_other 0.214 r_nbd_refined 0.21 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.174 r_ncsr_local_group_10 0.127 r_ncsr_local_group_2 0.122 r_ncsr_local_group_11 0.12 r_ncsr_local_group_13 0.114 r_ncsr_local_group_6 0.111 r_ncsr_local_group_12 0.109 r_ncsr_local_group_15 0.108 r_ncsr_local_group_3 0.105 r_ncsr_local_group_8 0.105 r_ncsr_local_group_7 0.099 r_ncsr_local_group_5 0.094 r_ncsr_local_group_1 0.093 r_ncsr_local_group_14 0.092 r_symmetry_nbtor_other 0.083 r_ncsr_local_group_4 0.083 r_ncsr_local_group_9 0.076 r_chiral_restr 0.066 r_symmetry_xyhbond_nbd_other 0.045 r_gen_planes_other 0.008 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7662 Nucleic Acid Atoms Solvent Atoms 518 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction autoPROC data scaling MOLREP phasing Coot model building