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Crystal structure of SETDB1 Tudor domain in complex with inhibitor XST06472A
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 7.2 295 25% PEG 3350, 0.2M LiSO4, 0.1M Bis-Tris pH6.5
Crystal Properties Matthews coefficient Solvent content 2.46 49.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.816 α = 90 b = 63.891 β = 90 c = 69.793 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 2013-10-03 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) Rrim I (All) Rpim I (All) 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 1.56 50 99 0.037 0.041 0.017 19.1 5.2 35386
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.59 87.1 0.471 3.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3DLM 1.56 47.13 34106 1121 98.99 0.1923 0.1914 0.2023 0.2185 0.2316 RANDOM 25.194
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] 0.74 -0.41 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.517 r_dihedral_angle_4_deg 17.387 r_dihedral_angle_3_deg 10.711 r_dihedral_angle_1_deg 6.451 r_mcangle_it 2.167 r_angle_refined_deg 1.403 r_mcbond_it 1.376 r_mcbond_other 1.375 r_angle_other_deg 0.891 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.517 r_dihedral_angle_4_deg 17.387 r_dihedral_angle_3_deg 10.711 r_dihedral_angle_1_deg 6.451 r_mcangle_it 2.167 r_angle_refined_deg 1.403 r_mcbond_it 1.376 r_mcbond_other 1.375 r_angle_other_deg 0.891 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1682 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 63
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction