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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 3IM8 PDB ENTRY 3IM8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.1 M TRIS-CL PH 8.0, 30% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.03 39.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.523 α = 90 b = 66.099 β = 90 c = 85.391 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 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 1.4 23.27 98.6 0.08 9.7 4.3 72439 1.6
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 1.4 4.43 95.5 0.44 2.5 3.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT PDB ENTRY 3IM8 1.4 22.45 68743 3647 100 0.17562 0.17411 0.20379 0.2245 RANDOM 21.307
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] 0.08 0.01 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.241 r_dihedral_angle_4_deg 16.71 r_dihedral_angle_3_deg 12.035 r_dihedral_angle_1_deg 5.659 r_scangle_it 5.574 r_scbond_it 3.457 r_mcangle_it 2.361 r_angle_refined_deg 2.194 r_mcbond_it 1.458 r_symmetry_vdw_refined 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.241 r_dihedral_angle_4_deg 16.71 r_dihedral_angle_3_deg 12.035 r_dihedral_angle_1_deg 5.659 r_scangle_it 5.574 r_scbond_it 3.457 r_mcangle_it 2.361 r_angle_refined_deg 2.194 r_mcbond_it 1.458 r_symmetry_vdw_refined 0.17 r_chiral_restr 0.14 r_xyhbond_nbd_refined 0.112 r_symmetry_hbond_refined 0.089 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_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 2733 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing