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Menin mutant - G331D in complex with Ziftomenib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GPQ
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 2.23 44.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.917 α = 90 b = 80.05 β = 90 c = 124.333 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 EIGER X 16M 2024-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.9795 NSLS-II 17-ID-2
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 1.45 40 99.9 0.08 40.61 10.7 86815
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 1.45 1.48 0.558 2.36 6.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.45 39.602 86731 4404 99.436 0.155 0.154 0.1548 0.1797 0.1804 20.475
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] 1.156 -0.201 -0.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.247 r_dihedral_angle_3_deg 12.153 r_dihedral_angle_2_deg 8.91 r_lrange_it 6.299 r_lrange_other 6.299 r_dihedral_angle_1_deg 5.995 r_scangle_it 4.817 r_scangle_other 4.816 r_mcangle_it 3.294 r_mcangle_other 3.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.247 r_dihedral_angle_3_deg 12.153 r_dihedral_angle_2_deg 8.91 r_lrange_it 6.299 r_lrange_other 6.299 r_dihedral_angle_1_deg 5.995 r_scangle_it 4.817 r_scangle_other 4.816 r_mcangle_it 3.294 r_mcangle_other 3.294 r_scbond_it 3.183 r_scbond_other 3.183 r_mcbond_it 2.151 r_mcbond_other 2.148 r_angle_refined_deg 2.032 r_angle_other_deg 0.691 r_symmetry_nbd_refined 0.268 r_nbd_refined 0.233 r_nbd_other 0.2 r_nbtor_refined 0.189 r_symmetry_nbd_other 0.181 r_symmetry_xyhbond_nbd_refined 0.174 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.11 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3737 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing