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Crystal Structure of DOT1L in Complex with EPZ-5676
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, SOAKING THE COMPOUND INTO CROSS-LINKED DOT1L-SAM CRYSTAL, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.37 63.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.43 α = 90 b = 154.43 β = 90 c = 47.52 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 IMAGE PLATE MAR scanner 300 mm plate 2010-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 1.07812 APS 21-ID-G
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 3.15 40.47 99.9 0.077 17.4 9 11501 11490 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 3.15 3.23 99.9 0.763 2.8 9 838
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 3QOW 3.15 40.47 10817 10813 674 99.96 0.18658 0.18266 0.179 0.2557 0.2643 RANDOM 121.57
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] -57.61 -57.61 115.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.622 r_dihedral_angle_4_deg 18.286 r_dihedral_angle_3_deg 17.832 r_dihedral_angle_1_deg 5.027 r_angle_refined_deg 1.044 r_chiral_restr 0.07 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.622 r_dihedral_angle_4_deg 18.286 r_dihedral_angle_3_deg 17.832 r_dihedral_angle_1_deg 5.027 r_angle_refined_deg 1.044 r_chiral_restr 0.07 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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 2605 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 51
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement MOSFLM data reduction Aimless data scaling