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Crystal Structure of SETDB1 Tudor domain in complex with UNC100013
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 20% PEG 8000, 0.2M NaCl, 0.1M HEPES pH 7.5, 5% Ethyl Glyceol
Crystal Properties Matthews coefficient Solvent content 2.3 46.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.153 α = 90 b = 55.132 β = 90 c = 118.367 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 1.53 50 100 0.087 0.091 0.026 0.996 8.2 12.2 37684
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 1.53 1.56 100 0.938 0.983 0.289 0.832 11.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.53 40.37 36104 1513 99.86 0.16308 0.16172 0.19463 0.2087 RANDOM 22.395
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] 1.02 -0.67 -0.35
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.222 r_long_range_B_other 12.108 r_dihedral_angle_3_deg 11.605 r_scangle_other 7.691 r_dihedral_angle_1_deg 6.741 r_mcangle_other 6.404 r_mcangle_it 6.401 r_scbond_it 5.036 r_scbond_other 5.034 r_mcbond_it 4.29
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.222 r_long_range_B_other 12.108 r_dihedral_angle_3_deg 11.605 r_scangle_other 7.691 r_dihedral_angle_1_deg 6.741 r_mcangle_other 6.404 r_mcangle_it 6.401 r_scbond_it 5.036 r_scbond_other 5.034 r_mcbond_it 4.29 r_mcbond_other 4.27 r_dihedral_angle_2_deg 3.21 r_rigid_bond_restr 2.081 r_angle_refined_deg 1.22 r_angle_other_deg 0.486 r_chiral_restr 0.069 r_gen_planes_refined 0.011 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 1752 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PHASER phasing HKL-3000 data reduction