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Architecture of a PKS-NRPS hybrid megaenzyme involved in the biosynthesis of the genotoxin colibactin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M MES pH 6.5, 19 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.68 54.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.643 α = 90 b = 233.374 β = 90 c = 256.598 γ = 90
Symmetry Space Group C 2 2 21
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 2021-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9655 ESRF MASSIF-1
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 2.98 49.395 93.6 0.138 0.996 9.5 2 114296
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 2.98 3.088 1.05 0.522 1.6
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 2.982 49.395 78289 1940 68.481 0.218 0.2171 0.2168 0.2384 0.2354 95.226
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] -1.03 0.709 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.367 r_dihedral_angle_6_deg 13.12 r_lrange_it 9.202 r_lrange_other 9.202 r_scangle_it 6.466 r_scangle_other 6.465 r_mcangle_it 6.021 r_mcangle_other 6.021 r_dihedral_angle_1_deg 5.87 r_dihedral_angle_2_deg 5.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.367 r_dihedral_angle_6_deg 13.12 r_lrange_it 9.202 r_lrange_other 9.202 r_scangle_it 6.466 r_scangle_other 6.465 r_mcangle_it 6.021 r_mcangle_other 6.021 r_dihedral_angle_1_deg 5.87 r_dihedral_angle_2_deg 5.011 r_scbond_it 3.944 r_scbond_other 3.944 r_mcbond_it 3.682 r_mcbond_other 3.682 r_angle_refined_deg 1.105 r_symmetry_xyhbond_nbd_refined 0.554 r_angle_other_deg 0.393 r_xyhbond_nbd_other 0.325 r_nbd_refined 0.261 r_nbd_other 0.249 r_symmetry_nbd_other 0.205 r_symmetry_nbd_refined 0.202 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.168 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.049 r_ncsr_local_group_6 0.046 r_ncsr_local_group_4 0.042 r_ncsr_local_group_2 0.04 r_ncsr_local_group_5 0.038 r_ncsr_local_group_1 0.037 r_ncsr_local_group_3 0.036 r_ncsr_local_group_7 0.023 r_symmetry_xyhbond_nbd_other 0.021 r_ext_dist_refined_b 0.01 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22022 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing