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Crystal Structure of the Curacin Biosynthetic Pathway HMG Synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YSL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 6% PEG 8000, 20 mM (NH4)2SO4, 1X MMT pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.36 63.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.162 α = 90 b = 101.162 β = 90 c = 106.234 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 2.1 87.61 100 0.112 1 15.5 19.5 37159 51.1
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 MOLECULAR REPLACEMENT THROUGHOUT 1YSL 2.1 87.61 35297 1826 99.97 0.1601 0.1585 0.1899 0.1906 RANDOM 58.407
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] 0.85 0.42 0.85 -2.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.384 r_dihedral_angle_4_deg 21.607 r_dihedral_angle_3_deg 13.488 r_dihedral_angle_1_deg 5.822 r_mcangle_it 3.589 r_mcbond_it 2.554 r_mcbond_other 2.55 r_angle_refined_deg 1.362 r_angle_other_deg 0.763 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.384 r_dihedral_angle_4_deg 21.607 r_dihedral_angle_3_deg 13.488 r_dihedral_angle_1_deg 5.822 r_mcangle_it 3.589 r_mcbond_it 2.554 r_mcbond_other 2.55 r_angle_refined_deg 1.362 r_angle_other_deg 0.763 r_chiral_restr 0.08 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 3133 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing