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Crystal structure of SETDB1 with a modified H3 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other similar, nearly isomorphous crystal structure, to be published
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 2.32 47.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.258 α = 90 b = 72.448 β = 104.84 c = 52.505 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315r 2013-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9686 APS 19-ID
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 1.25 41.57 99.8 0.05 0.059 0.03 0.999 15.1 3.7 74273
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 99.8 1.018 1.198 0.625 0.487 3.6 3645
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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT similar, nearly isomorphous crystal structure, to be published 1.25 41.57 70524 3722 99.8 0.1492 0.1474 0.1588 0.1829 0.1909 16.006
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] -0.17 -0.06 0.32 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.886 r_sphericity_free 19.119 r_dihedral_angle_4_deg 17.305 r_dihedral_angle_3_deg 12.186 r_sphericity_bonded 8.964 r_dihedral_angle_1_deg 6.949 r_mcangle_it 4.028 r_mcbond_it 3.228 r_mcbond_other 3.224 r_rigid_bond_restr 2.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.886 r_sphericity_free 19.119 r_dihedral_angle_4_deg 17.305 r_dihedral_angle_3_deg 12.186 r_sphericity_bonded 8.964 r_dihedral_angle_1_deg 6.949 r_mcangle_it 4.028 r_mcbond_it 3.228 r_mcbond_other 3.224 r_rigid_bond_restr 2.955 r_angle_refined_deg 1.937 r_angle_other_deg 1.106 r_chiral_restr 0.127 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1805 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing