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Crystal Structure of the Acyltransferase Domain of the Iterative Polyketide Synthase in Enediyne Biosynthesis Reveals the Molecular Basis of Substrate Specificity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AMM PDB ENTRY 4AMM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 0.1M TRIS-CL PH8.0, 30% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.06 40.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.714 α = 90 b = 66.245 β = 90 c = 86.086 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 287 PIXEL DECTRIS PIXEL PILATUS 2M-F COLLIMATOR 2011-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.65 26.33 99.4 0.07 11.1 4.7 45596 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.65 99.5 0.52 2.8 4.8
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 PDB ENTRY 4AMM 1.65 52.5 43232 2298 99.13 0.17552 0.17352 0.1746 0.21335 0.2145 RANDOM 24.924
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] 0.93 0.15 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.136 r_dihedral_angle_4_deg 17.452 r_dihedral_angle_3_deg 14.377 r_scangle_it 5.898 r_dihedral_angle_1_deg 5.669 r_scbond_it 3.671 r_mcangle_it 2.514 r_angle_refined_deg 2.137 r_mcbond_it 1.523 r_symmetry_vdw_refined 0.236
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.136 r_dihedral_angle_4_deg 17.452 r_dihedral_angle_3_deg 14.377 r_scangle_it 5.898 r_dihedral_angle_1_deg 5.669 r_scbond_it 3.671 r_mcangle_it 2.514 r_angle_refined_deg 2.137 r_mcbond_it 1.523 r_symmetry_vdw_refined 0.236 r_chiral_restr 0.154 r_symmetry_hbond_refined 0.148 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2648 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement GO.COM data reduction SCALA data scaling