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Crystal Structure of DOT1L in Complex with EPZ003696
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QOW PDB ENTRY 3QOW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 293 100 mM Sodium Acetate, 1.8-2.0 M Ammonium Sulfate, 5 mM TCEP, pH 5.2, soaking the compound into cross-linked DOT1L-SAM crystal, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.63 66.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.6 α = 90 b = 157.6 β = 90 c = 49.15 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 100 CCD MARMOSAIC 225 mm CCD 2009-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.8 41.7 100 0.094 11.8 6.1 17520 17520 1
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 2.8 2.95 99.9 0.421 3.5 5.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3QOW 2.8 41.7 16612 886 99.93 0.21287 0.21035 0.26109 0.2254 RANDOM 74.056
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] -0.13 -0.07 -0.13 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.621 r_dihedral_angle_4_deg 21.079 r_dihedral_angle_3_deg 17.686 r_dihedral_angle_1_deg 6.126 r_angle_refined_deg 1.291 r_chiral_restr 0.092 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.621 r_dihedral_angle_4_deg 21.079 r_dihedral_angle_3_deg 17.686 r_dihedral_angle_1_deg 6.126 r_angle_refined_deg 1.291 r_chiral_restr 0.092 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2594 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 37
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement MOSFLM data reduction