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Menin mutant G331D 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 44.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.082 α = 90 b = 80.217 β = 90 c = 124.926 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 1.469 50 99.9 0.103 33.083 7.3 84613
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 1.469 1.5 0.923 2.09 7.2
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-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.47 27.83 84536 4080 99.7 0.16 0.188 0.1845 20.66
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] 0.279 -0.059 -0.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.999 r_dihedral_angle_2_deg 9.823 r_dihedral_angle_1_deg 5.903 r_scangle_it 4.847 r_scangle_other 4.846 r_scbond_other 3.247 r_scbond_it 3.246 r_mcangle_it 3.037 r_mcangle_other 3.036 r_mcbond_other 2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.999 r_dihedral_angle_2_deg 9.823 r_dihedral_angle_1_deg 5.903 r_scangle_it 4.847 r_scangle_other 4.846 r_scbond_other 3.247 r_scbond_it 3.246 r_mcangle_it 3.037 r_mcangle_other 3.036 r_mcbond_other 2.11 r_mcbond_it 2.109 r_angle_refined_deg 1.914 r_angle_other_deg 0.669 r_nbd_refined 0.23 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.154 r_nbd_other 0.145 r_chiral_restr 0.104 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbtor_other 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_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3741 Nucleic Acid Atoms Solvent Atoms 531 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing