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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 2.60 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 2.78 55.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.271 α = 90 b = 79.846 β = 93.354 c = 107.541 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 2.6 69.12 98.1 0.167 0.162 0.925 3.8 3.3 35497
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 2.6 2.72 87.6 1.059 1.01 0.44 0.7
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 2.6 59.736 35413 699 97.815 0.228 0.2271 0.2341 0.2702 0.2703 58.65
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] 4.066 0.314 0.67 -4.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.154 r_dihedral_angle_3_deg 13.726 r_lrange_it 12.927 r_lrange_other 12.905 r_scangle_it 7.709 r_scangle_other 7.708 r_dihedral_angle_2_deg 7.654 r_mcangle_other 7.115 r_mcangle_it 7.114 r_dihedral_angle_1_deg 5.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.154 r_dihedral_angle_3_deg 13.726 r_lrange_it 12.927 r_lrange_other 12.905 r_scangle_it 7.709 r_scangle_other 7.708 r_dihedral_angle_2_deg 7.654 r_mcangle_other 7.115 r_mcangle_it 7.114 r_dihedral_angle_1_deg 5.91 r_scbond_it 4.627 r_scbond_other 4.621 r_mcbond_it 4.41 r_mcbond_other 4.409 r_angle_refined_deg 1.418 r_angle_other_deg 0.813 r_nbd_other 0.225 r_symmetry_nbd_other 0.208 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.199 r_symmetry_nbd_refined 0.192 r_nbtor_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.156 r_symmetry_xyhbond_nbd_other 0.141 r_ncsr_local_group_14 0.12 r_ncsr_local_group_9 0.119 r_ncsr_local_group_15 0.117 r_ncsr_local_group_5 0.114 r_ncsr_local_group_12 0.113 r_ncsr_local_group_6 0.093 r_ncsr_local_group_13 0.091 r_ncsr_local_group_1 0.089 r_ncsr_local_group_10 0.089 r_ncsr_local_group_3 0.087 r_ncsr_local_group_8 0.087 r_ncsr_local_group_7 0.083 r_ncsr_local_group_11 0.083 r_symmetry_nbtor_other 0.079 r_ncsr_local_group_4 0.079 r_chiral_restr 0.068 r_ncsr_local_group_2 0.055 r_bond_refined_d 0.006 r_gen_planes_other 0.006 r_gen_planes_refined 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 456 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction autoPROC data scaling MOLREP phasing Coot model building