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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 2.65 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 2.72 54.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.929 α = 90 b = 78.643 β = 93.117 c = 107.005 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 2.651 42.64 94.4 0.089 0.984 5 2.1 31523 38.3
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 2.651 2.697 96.3 0.299 0.842 2.2 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.651 42.64 31523 1535 94.42 0.173 0.1705 0.1757 0.2345 0.2374 44.264
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] 1.708 0.325 1.196 -2.922
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.764 r_dihedral_angle_3_deg 13.194 r_lrange_other 10.126 r_lrange_it 10.124 r_dihedral_angle_2_deg 7.729 r_scangle_it 6.465 r_scangle_other 6.465 r_dihedral_angle_1_deg 6.304 r_mcangle_it 5.666 r_mcangle_other 5.666
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.764 r_dihedral_angle_3_deg 13.194 r_lrange_other 10.126 r_lrange_it 10.124 r_dihedral_angle_2_deg 7.729 r_scangle_it 6.465 r_scangle_other 6.465 r_dihedral_angle_1_deg 6.304 r_mcangle_it 5.666 r_mcangle_other 5.666 r_scbond_it 3.882 r_scbond_other 3.882 r_mcbond_it 3.46 r_mcbond_other 3.46 r_angle_refined_deg 1.408 r_angle_other_deg 0.74 r_nbd_other 0.268 r_symmetry_xyhbond_nbd_refined 0.245 r_symmetry_nbd_other 0.213 r_nbd_refined 0.208 r_symmetry_nbd_refined 0.187 r_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.175 r_symmetry_xyhbond_nbd_other 0.145 r_xyhbond_nbd_other 0.104 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.062 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 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 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