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Crystal Structure of SETDB1 Tudor domain in complex with UNC100016
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DLM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 25% P3350, 0.1M NH4SO4, 0.1M Bis-Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.13 42.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.834 α = 90 b = 60.663 β = 90 c = 70.007 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 PIXEL DECTRIS PILATUS3 S 6M 2023-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.18061 CLSI 08B1-1
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 1.27 50 100 0.052 0.054 0.016 1 11.3 11.7 60159
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 1.27 1.29 99.9 0.916 0.974 0.325 0.719 8.5
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 MOLECULAR REPLACEMENT THROUGHOUT 1.27 45.89 57040 3050 99.8 0.16004 0.15892 0.1751 0.18119 0.1885 RANDOM 13.168
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] 0.87 -1.1 0.23
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 11.889 r_dihedral_angle_3_deg 10.324 r_long_range_B_other 9.742 r_dihedral_angle_1_deg 6.805 r_scangle_other 4.624 r_mcangle_other 4.134 r_mcangle_it 4.133 r_dihedral_angle_2_deg 3.973 r_scbond_it 2.992 r_scbond_other 2.991
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 11.889 r_dihedral_angle_3_deg 10.324 r_long_range_B_other 9.742 r_dihedral_angle_1_deg 6.805 r_scangle_other 4.624 r_mcangle_other 4.134 r_mcangle_it 4.133 r_dihedral_angle_2_deg 3.973 r_scbond_it 2.992 r_scbond_other 2.991 r_mcbond_it 2.554 r_mcbond_other 2.547 r_rigid_bond_restr 1.768 r_angle_refined_deg 1.269 r_angle_other_deg 0.494 r_chiral_restr 0.07 r_gen_planes_refined 0.013 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1769 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PHASER phasing HKL-3000 data reduction