☰ Navigation Tabs
Structural insights into inhibition of the bivalent menin-MLL interaction by small molecules in leukemia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RE2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG
3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM
Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data collection,
crystals were transferred into a cryo-solution containing 20% PEG550
MME and flash-frozen in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.24 44.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.812 α = 90 b = 80.178 β = 90 c = 124.686 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 CCD MARMOSAIC 300 mm CCD M SINGLE WAVELENGTH 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D APS 21-ID-D 2 APS 21-ID-F
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 1.46 36.9 99.4 0.11 16.1 6.8 85179
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 1.46 1.49 88.1 0.361 4.5 5.6
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 3RE2 1.46 36.9 80382 4236 99.31 0.14617 0.14459 0.1426 0.17555 0.1745 RANDOM 18.124
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] -0.01 0.05 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.51 r_dihedral_angle_4_deg 14.522 r_sphericity_bonded 12.796 r_dihedral_angle_3_deg 11.543 r_dihedral_angle_1_deg 5.06 r_rigid_bond_restr 3.256 r_angle_refined_deg 1.192 r_chiral_restr 0.083 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3689 Nucleic Acid Atoms Solvent Atoms 586 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement