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Menin mutant - G331R 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 2.24 45.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.083 α = 90 b = 80.126 β = 90 c = 124.82 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 9M 2023-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 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 1.246 67.43 100 0.092 16 13.1 138049
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 1.25 1.31 100 1.079 2.5 11.1
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 1.25 67.429 136628 6986 99.997 0.147 0.1456 0.1436 0.1719 0.1713 15.855
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] -0.844 -0.758 1.602
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.817 r_lrange_other 11.346 r_lrange_it 11.304 r_dihedral_angle_3_deg 11.287 r_dihedral_angle_2_deg 10.255 r_scangle_it 9.927 r_scangle_other 9.926 r_mcangle_other 7.29 r_mcangle_it 7.286 r_scbond_other 7.273
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.817 r_lrange_other 11.346 r_lrange_it 11.304 r_dihedral_angle_3_deg 11.287 r_dihedral_angle_2_deg 10.255 r_scangle_it 9.927 r_scangle_other 9.926 r_mcangle_other 7.29 r_mcangle_it 7.286 r_scbond_other 7.273 r_scbond_it 7.248 r_rigid_bond_restr 7.112 r_dihedral_angle_1_deg 5.952 r_mcbond_other 5.053 r_mcbond_it 5.052 r_angle_refined_deg 1.928 r_angle_other_deg 0.698 r_nbd_refined 0.227 r_symmetry_nbd_refined 0.218 r_nbd_other 0.202 r_nbtor_refined 0.186 r_symmetry_nbd_other 0.183 r_xyhbond_nbd_refined 0.14 r_symmetry_xyhbond_nbd_refined 0.135 r_chiral_restr 0.112 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3695 Nucleic Acid Atoms Solvent Atoms 563 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing