☰ Navigation Tabs
Crystal structure of SETDB1 with a modified H3 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BHE earlier version of coordinates of nearly isomorphous crystal structure (see PDB entry 6BHE)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 291 20% PEG5000 MME, 0.1 M Bis-Tris
Crystal Properties Matthews coefficient Solvent content 2.35 47.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.709 α = 90 b = 72.363 β = 104.75 c = 52.501 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 MARMOSAIC 300 mm CCD 2013-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97944 APS 23-ID-B
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 41.56 99.3 0.035 0.042 0.022 1 19.9 3.7 53270
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 93.1 0.826 1.025 0.594 0.591 2.8 2436
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 coordinates of nearly isomorphous crystal structure (see PDB entry 6BHE) 1.45 41.56 45714 2428 99.65 0.1352 0.133 0.1484 0.1761 0.1847 20.631
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] 0.59 -0.42 -0.29 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.706 r_sphericity_free 26.859 r_dihedral_angle_4_deg 15.85 r_sphericity_bonded 13.059 r_dihedral_angle_3_deg 10.372 r_dihedral_angle_1_deg 6.509 r_mcangle_it 3.049 r_mcbond_it 2.65 r_mcbond_other 2.563 r_rigid_bond_restr 2.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.706 r_sphericity_free 26.859 r_dihedral_angle_4_deg 15.85 r_sphericity_bonded 13.059 r_dihedral_angle_3_deg 10.372 r_dihedral_angle_1_deg 6.509 r_mcangle_it 3.049 r_mcbond_it 2.65 r_mcbond_other 2.563 r_rigid_bond_restr 2.185 r_angle_refined_deg 1.662 r_angle_other_deg 0.996 r_chiral_restr 0.111 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1750 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing