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Crystal Structure of the Curacin Biosynthetic Pathway HMG Synthase in Complex with Holo Donor-ACP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KP5 5KP5 and 5KP6 experimental model PDB 5KP6 5KP5 and 5KP6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 10% PEG 8000, 120 mM (NH4)2SO4, 1X MMT pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.78 55.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.117 α = 90 b = 101.117 β = 90 c = 104.595 γ = 120
Symmetry Space Group P 31 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 PILATUS3 6M 2014-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
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 1.6 87.57 100 0.116 1 16.9 19.8 81779 23.9
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 5KP5 and 5KP6 1.6 87.57 77704 4031 99.99 0.1518 0.1511 0.1639 0.1668 0.1749 RANDOM 34.237
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] 0.21 0.1 0.21 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.944 r_dihedral_angle_4_deg 20.324 r_dihedral_angle_3_deg 12.641 r_dihedral_angle_1_deg 5.718 r_angle_refined_deg 1.537 r_mcangle_it 1.459 r_angle_other_deg 0.964 r_mcbond_it 0.848 r_mcbond_other 0.846 r_chiral_restr 0.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.944 r_dihedral_angle_4_deg 20.324 r_dihedral_angle_3_deg 12.641 r_dihedral_angle_1_deg 5.718 r_angle_refined_deg 1.537 r_mcangle_it 1.459 r_angle_other_deg 0.964 r_mcbond_it 0.848 r_mcbond_other 0.846 r_chiral_restr 0.159 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3813 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling REFMAC phasing