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Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the 17-mer expression tag bound in the substrate binding site of a neighbouring molecule at 2.10 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 2.62 53.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.308 α = 90 b = 78.676 β = 93.249 c = 106.797 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 EIGER2 X 9M 2023-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8731 ESRF ID30B
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 2.1 49.29 98.7 0.115 0.109 0.995 6.2 3.4 65468 36.9
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 2.1 2.15 1.438 1.35 0.268 0.6
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 2.101 43.325 65461 1302 98.651 0.225 0.2238 0.2297 0.2775 0.2765 49.913
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] 2.48 -0.466 0.461 -2.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.444 r_dihedral_angle_3_deg 13.566 r_lrange_other 9.949 r_lrange_it 9.942 r_dihedral_angle_2_deg 6.897 r_scangle_it 6.891 r_scangle_other 6.891 r_dihedral_angle_1_deg 6.337 r_mcangle_other 5.94 r_mcangle_it 5.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.444 r_dihedral_angle_3_deg 13.566 r_lrange_other 9.949 r_lrange_it 9.942 r_dihedral_angle_2_deg 6.897 r_scangle_it 6.891 r_scangle_other 6.891 r_dihedral_angle_1_deg 6.337 r_mcangle_other 5.94 r_mcangle_it 5.939 r_scbond_it 4.245 r_scbond_other 4.237 r_mcbond_it 3.843 r_mcbond_other 3.84 r_angle_refined_deg 1.41 r_angle_other_deg 0.756 r_symmetry_nbd_refined 0.263 r_nbd_other 0.219 r_nbd_refined 0.218 r_symmetry_nbd_other 0.213 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.178 r_xyhbond_nbd_refined 0.176 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.062 r_symmetry_xyhbond_nbd_other 0.05 r_xyhbond_nbd_other 0.011 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7702 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction autoPROC data scaling MOLREP phasing Coot model building