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Crystal structure of type III polyketide synthase from Mycobacterium marinum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20% (w/v) Polyethylene glycol 3000 and
100 mM HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.48 64.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.407 α = 90 b = 131.407 β = 90 c = 187.187 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2016-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95372 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.306 72.287 90.4 0.058 0.064 0.027 0.999 17.9 5.4 28212
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.306 2.487 68 0.56 0.747 0.487 0.576 1.4 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1TED 2.31 72.287 26660 1552 53.05 0.19896 0.19787 0.2022 0.21743 0.2226 RANDOM 58.669
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] 1.2 0.6 1.2 -3.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.763 r_dihedral_angle_4_deg 21.927 r_dihedral_angle_3_deg 15.275 r_dihedral_angle_1_deg 6.29 r_long_range_B_refined 5.719 r_long_range_B_other 5.719 r_scangle_other 2.741 r_mcangle_it 2.295 r_mcangle_other 2.295 r_scbond_it 1.718
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.763 r_dihedral_angle_4_deg 21.927 r_dihedral_angle_3_deg 15.275 r_dihedral_angle_1_deg 6.29 r_long_range_B_refined 5.719 r_long_range_B_other 5.719 r_scangle_other 2.741 r_mcangle_it 2.295 r_mcangle_other 2.295 r_scbond_it 1.718 r_scbond_other 1.718 r_angle_refined_deg 1.524 r_mcbond_it 1.4 r_mcbond_other 1.386 r_angle_other_deg 0.973 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5263 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data processing Aimless data scaling PHASER phasing