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Crystal Structure of SETDB1 Tudor domain in complexed with (R,R)-59
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BHD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.1%w/v n-Octyl-B-D-glucoside
0.1 M Sodium citrate trihydrate,pH 5.5
22% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.84 56.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.335 α = 90 b = 69.214 β = 98.93 c = 110.124 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 2020-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97918 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.47 58.4 99.7 0.997 12.1 6.6 29988
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.475 2.731 0.485
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 6BHD 2.474 41.162 1.34 29958 1473 67.27 0.2078 0.2043 0.2067 0.2764 0.2789
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.868 f_angle_d 1.559 f_chiral_restr 0.068 f_bond_d 0.016 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6826 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 264
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing