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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 PDB 6BHD earlier version of model from PDB entry 6BHD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 25% PEG3350, 0.2 M lithium sulfate, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.36 47.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.849 α = 90 b = 71.718 β = 104.48 c = 52.69 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 2013-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 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 1.4 41.57 99.7 0.065 0.076 0.04 0.998 12.5 3.6 53403
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 1.4 1.42 100 0.942 1.104 0.57 0.541 3.7 2726
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 earlier version of model from PDB entry 6BHD 1.4 41.57 50707 2671 99.52 0.1496 0.1476 0.1589 0.1872 0.1971 17.643
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] 0.01 -0.29 0.05 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.164 r_sphericity_free 22.424 r_dihedral_angle_4_deg 15.268 r_dihedral_angle_3_deg 11.661 r_sphericity_bonded 9.88 r_dihedral_angle_1_deg 6.875 r_mcangle_it 2.929 r_mcbond_it 2.577 r_mcbond_other 2.577 r_rigid_bond_restr 2.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.164 r_sphericity_free 22.424 r_dihedral_angle_4_deg 15.268 r_dihedral_angle_3_deg 11.661 r_sphericity_bonded 9.88 r_dihedral_angle_1_deg 6.875 r_mcangle_it 2.929 r_mcbond_it 2.577 r_mcbond_other 2.577 r_rigid_bond_restr 2.294 r_angle_refined_deg 1.82 r_angle_other_deg 1.014 r_chiral_restr 0.119 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1763 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing