☰ Navigation Tabs
Crystal structure of SMYD2 in complex with two PARP1 peptides
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WUY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20% PEG3350, 100 mM Tris pH 7.5, 5% ethanol, 1 mM PARP1 peptide, 0.6 mM AdoHcy
Crystal Properties Matthews coefficient Solvent content 2.37 48.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.792 α = 90 b = 52.185 β = 113.242 c = 144.916 γ = 90
Symmetry Space Group C 1 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 CCD MARMOSAIC 225 mm CCD 2017-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97856 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.1 133.16 88.6 0.105 0.114 0.042 0.995 13.7 7.3 57685 32.26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.137 96.7 0.862 0.505 0.772 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.1 66.58 0.31 51079 2578 88.57 0.1851 0.1839 0.1873 0.2079 0.213 47.37
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.1482 f_angle_d 0.718 f_chiral_restr 0.0463 f_plane_restr 0.0045 f_bond_d 0.0042
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7067 Nucleic Acid Atoms Solvent Atoms 420 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing