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Crystal Structure of Human DOT1L in Complex with a Selective Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NW3 PDB ENTRY 1NW3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.3 295 PROTEIN SOLUTION: 20 mM Tris, pH 8.0, 200 mM NaCl, 1 mM EDTA, 10% glycerol, 3 mM inhibitor, 3 mM TCEP. RESERVOIR SOLUTION: 0.1 M HAC, pH 5.3, 1.25-1.7 M (NH4)2SO4. , VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 4.21 70.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.753 α = 90 b = 152.753 β = 90 c = 50.889 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 IMAGE PLATE RIGAKU RAXIS HTC MIRRORS 2011-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.5 100 96.9 0.14 18 12.9 23777 23040 63
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 100 0.863 3 13 1232
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1NW3 2.5 30.55 23823 23019 1154 96.6 0.234 0.234 0.2341 0.274 0.2735 RANDOM 64.1
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] -8.77 -8.77 17.54
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.9 c_scangle_it 3.5 c_mcangle_it 2.82 c_scbond_it 2.26 c_mcbond_it 1.62 c_angle_deg 1.3 c_improper_angle_d 0.81 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2671 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 42
Software Software Software Name Purpose StructureStudio data collection PHASER phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling