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Crystal Structure of SETDB1 Tudor domain in complex with UNC6535
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KE2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 20% (w/v) PEG8000, 0.2M Sodium Chloride, 0.1M Hepes, pH 7.5, 5% MPD
Crystal Properties Matthews coefficient Solvent content 2.21 44.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.056 α = 90 b = 61.997 β = 90 c = 69.335 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKU SATURN A200 2020-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.98 50 97.2 0.102 0.993 16 5 16327
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.01 90 0.677 0.724 1.8 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.98 31.02 15452 841 97.22 0.20333 0.20091 0.2118 0.24856 0.2595 RANDOM 26.015
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] 1.38 -0.73 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.161 r_dihedral_angle_4_deg 17.753 r_dihedral_angle_3_deg 12.839 r_dihedral_angle_1_deg 8.253 r_long_range_B_refined 5.631 r_long_range_B_other 5.616 r_scangle_other 3.959 r_mcangle_it 3.324 r_mcangle_other 3.323 r_scbond_it 2.581
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.161 r_dihedral_angle_4_deg 17.753 r_dihedral_angle_3_deg 12.839 r_dihedral_angle_1_deg 8.253 r_long_range_B_refined 5.631 r_long_range_B_other 5.616 r_scangle_other 3.959 r_mcangle_it 3.324 r_mcangle_other 3.323 r_scbond_it 2.581 r_scbond_other 2.58 r_mcbond_it 2.264 r_mcbond_other 2.263 r_angle_refined_deg 1.368 r_angle_other_deg 1.228 r_chiral_restr 0.059 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1714 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 40
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement HKL-3000 data reduction REFMAC phasing