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Wild-type Menin complexed with DS-1594
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7UJ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 22%(w/v) PEG3350, 0.2M MAGNESIUM NITRATE, 0.1 M HEPES PH=7.8, 20%(v/v) ETHYLENE GLYCOL, VAPOR
DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.26 45.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.786 α = 90 b = 78.646 β = 101.51 c = 92.615 γ = 90
Symmetry Space Group P 1 21 1
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 2022-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953739 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.626 48.12 97.9 0.998 16 7 120522
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.626 1.65 89.4 0.93 4.5 3.4
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 7UJ4 1.63 48.12 114372 6005 97.63 0.15491 0.15376 0.1677 0.17634 0.185 RANDOM 14.433
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] 0.25 -0.86 -0.5 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.863 r_dihedral_angle_4_deg 18.562 r_dihedral_angle_3_deg 13.888 r_dihedral_angle_1_deg 5.996 r_long_range_B_refined 5.634 r_long_range_B_other 5.514 r_scangle_other 4.323 r_scbond_it 2.775 r_scbond_other 2.775 r_mcangle_it 2.479
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.863 r_dihedral_angle_4_deg 18.562 r_dihedral_angle_3_deg 13.888 r_dihedral_angle_1_deg 5.996 r_long_range_B_refined 5.634 r_long_range_B_other 5.514 r_scangle_other 4.323 r_scbond_it 2.775 r_scbond_other 2.775 r_mcangle_it 2.479 r_mcangle_other 2.479 r_angle_refined_deg 1.802 r_mcbond_it 1.643 r_mcbond_other 1.643 r_angle_other_deg 1.575 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7221 Nucleic Acid Atoms Solvent Atoms 682 Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling PHASER phasing PDB_EXTRACT data extraction