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Crystal Structure of the Curacin Biosynthetic Pathway HMG Synthase in Complex with Apo Donor-ACP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KP5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 6% PEG 8000, 60 mM (NH4)2SO4, 1X MMT pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.8 56.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.312 α = 90 b = 101.312 β = 90 c = 104.593 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 2.05 87.74 100 0.117 0.99 19.1 19.5 39403 37
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 2.05 87.74 37444 1926 99.95 0.1572 0.1553 0.1654 0.1932 0.1995 RANDOM 49.469
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] 0.47 0.24 0.47 -1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.287 r_dihedral_angle_4_deg 21.599 r_dihedral_angle_3_deg 14.339 r_dihedral_angle_1_deg 5.65 r_mcangle_it 2.996 r_mcbond_it 2.108 r_mcbond_other 2.098 r_angle_refined_deg 1.476 r_angle_other_deg 0.776 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.287 r_dihedral_angle_4_deg 21.599 r_dihedral_angle_3_deg 14.339 r_dihedral_angle_1_deg 5.65 r_mcangle_it 2.996 r_mcbond_it 2.108 r_mcbond_other 2.098 r_angle_refined_deg 1.476 r_angle_other_deg 0.776 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3747 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling REFMAC phasing