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Crystal Structure of the Curacin Biosynthetic Pathway HMG Synthase in Complex with Acetyl Donor-ACP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KP5 5KP5, 5KP6 experimental model PDB 5KP6 5KP5, 5KP6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 6% PEG 8000, 100 mM (NH4)2SO4, 1X MMT pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.77 55.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.892 α = 90 b = 100.892 β = 90 c = 104.461 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) 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 1.9 87.38 100 0.116 16.9 19.5 48869 29.6
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 FOURIER SYNTHESIS THROUGHOUT 5KP5, 5KP6 1.9 87.38 48869 2374 100 0.158 0.157 0.1664 0.182 0.1855 RANDOM 39.1
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] 0.25 0.12 0.25 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.229 r_dihedral_angle_4_deg 18.522 r_dihedral_angle_3_deg 13.626 r_dihedral_angle_1_deg 5.558 r_mcangle_it 2.176 r_mcbond_it 1.405 r_mcbond_other 1.403 r_angle_refined_deg 1.352 r_angle_other_deg 0.767 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.229 r_dihedral_angle_4_deg 18.522 r_dihedral_angle_3_deg 13.626 r_dihedral_angle_1_deg 5.558 r_mcangle_it 2.176 r_mcbond_it 1.405 r_mcbond_other 1.403 r_angle_refined_deg 1.352 r_angle_other_deg 0.767 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 3805 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling