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Menin mutant T349M in complex with MLL peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 285 0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Crystal Properties Matthews coefficient Solvent content 2.2 44.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.045 α = 90 b = 80.235 β = 90 c = 125.085 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 CCD MARMOSAIC 300 mm CCD 2023-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 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 1.569 50 100 0.15 20.952 7 69845
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 1.569 1.6 0.963 2.03 5.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.569 29.153 69771 3548 99.883 0.162 0.1598 0.1971 0.1887 18.289
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] 0.533 -0.228 -0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.386 r_dihedral_angle_3_deg 11.831 r_dihedral_angle_2_deg 8.145 r_dihedral_angle_1_deg 6.167 r_lrange_it 5.959 r_lrange_other 5.805 r_scangle_it 4.367 r_scangle_other 4.367 r_scbond_it 2.905 r_scbond_other 2.905
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.386 r_dihedral_angle_3_deg 11.831 r_dihedral_angle_2_deg 8.145 r_dihedral_angle_1_deg 6.167 r_lrange_it 5.959 r_lrange_other 5.805 r_scangle_it 4.367 r_scangle_other 4.367 r_scbond_it 2.905 r_scbond_other 2.905 r_mcangle_it 2.771 r_mcangle_other 2.77 r_mcbond_it 1.863 r_mcbond_other 1.86 r_angle_refined_deg 1.852 r_dihedral_angle_other_2_deg 1.462 r_angle_other_deg 0.648 r_symmetry_nbd_refined 0.233 r_nbd_refined 0.228 r_symmetry_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.185 r_nbd_other 0.185 r_symmetry_nbd_other 0.181 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_symmetry_xyhbond_nbd_other 0.006 r_bond_other_d 0.001 r_chiral_restr_other 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3735 Nucleic Acid Atoms Solvent Atoms 503 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing