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Wild-type Menin complexed with KO-539
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 24%(w/v) PEG3350, 0.2M MAGNESIUM NITRATE, 0.1M HEPES PH=7.8, 20%(v/v) ETHYLENE GLYCOL,
PH7.8
Crystal Properties Matthews coefficient Solvent content 2.31 46.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.089 α = 90 b = 78.852 β = 101.54 c = 93.34 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 2021-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953651 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 2.348 48.34 99 0.985 5.8 3.5 41354
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 2.35 2.43 0.524
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 2.4 48.34 37227 1910 99.97 0.21123 0.20795 0.2142 0.27471 0.2784 RANDOM 33.031
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] -0.59 -0.41 -0.64 1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.531 r_dihedral_angle_3_deg 17.279 r_dihedral_angle_4_deg 15.471 r_dihedral_angle_1_deg 6.762 r_long_range_B_refined 6.457 r_long_range_B_other 6.437 r_scangle_other 4.089 r_mcangle_it 3.743 r_mcangle_other 3.743 r_scbond_other 2.449
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.531 r_dihedral_angle_3_deg 17.279 r_dihedral_angle_4_deg 15.471 r_dihedral_angle_1_deg 6.762 r_long_range_B_refined 6.457 r_long_range_B_other 6.437 r_scangle_other 4.089 r_mcangle_it 3.743 r_mcangle_other 3.743 r_scbond_other 2.449 r_scbond_it 2.448 r_mcbond_it 2.295 r_mcbond_other 2.295 r_angle_refined_deg 1.443 r_angle_other_deg 1.233 r_chiral_restr 0.236 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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 7193 Nucleic Acid Atoms Solvent Atoms 425 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction pointless data scaling MOLREP phasing