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Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OOI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1M Hepes, PH7.3, 0.1MKSCN, 25-30%MPEG2000
Crystal Properties Matthews coefficient Solvent content 2.06 40.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.983 α = 90 b = 61.504 β = 90 c = 77.308 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 PIXEL DECTRIS PILATUS3 S 6M 2013-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.62 46.893 90.9 13.6 5.3 182683
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 FOURIER SYNTHESIS THROUGHOUT 3OOI 1.62 46.89 31691 1659 90.84 0.18304 0.1813 0.1915 0.21469 0.2206 RANDOM 20.258
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] -0.02 0.06 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.478 r_dihedral_angle_4_deg 16.593 r_dihedral_angle_3_deg 13.146 r_dihedral_angle_1_deg 6.023 r_long_range_B_refined 4.691 r_long_range_B_other 4.687 r_scbond_it 1.78 r_scbond_other 1.78 r_angle_refined_deg 1.483 r_mcbond_it 1.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.478 r_dihedral_angle_4_deg 16.593 r_dihedral_angle_3_deg 13.146 r_dihedral_angle_1_deg 6.023 r_long_range_B_refined 4.691 r_long_range_B_other 4.687 r_scbond_it 1.78 r_scbond_other 1.78 r_angle_refined_deg 1.483 r_mcbond_it 1.256 r_mcbond_other 1.193 r_angle_other_deg 0.939 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_bond_other_d 0.002 r_gen_planes_refined 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_mcangle_it r_mcangle_other r_scangle_it r_scangle_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1964 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing