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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 3DLM PDB entry 3DLM
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 2.26 45.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.051 α = 90 b = 71.372 β = 104.23 c = 52.055 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 2013-07-10 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97856 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 1.33 41.2 99.8 0.049 0.057 0.03 0.999 15.3 3.7 60118
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 1.33 1.35 99.9 1.153 1.354 0.703 0.495 3.6 2964
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3DLM 1.35 35.69 54617 2872 99.76 0.1364 0.1345 0.1497 0.1725 0.1835 19.566
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] -0.15 -0.29 -0.03 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.815 r_sphericity_free 26.815 r_dihedral_angle_4_deg 17.422 r_sphericity_bonded 11.976 r_dihedral_angle_3_deg 11.549 r_dihedral_angle_1_deg 6.944 r_mcangle_it 2.887 r_mcbond_other 2.472 r_mcbond_it 2.469 r_rigid_bond_restr 2.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.815 r_sphericity_free 26.815 r_dihedral_angle_4_deg 17.422 r_sphericity_bonded 11.976 r_dihedral_angle_3_deg 11.549 r_dihedral_angle_1_deg 6.944 r_mcangle_it 2.887 r_mcbond_other 2.472 r_mcbond_it 2.469 r_rigid_bond_restr 2.153 r_angle_refined_deg 1.755 r_angle_other_deg 1.017 r_chiral_restr 0.114 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1791 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing