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Wild-type Menin complexed with JNJ-75276617
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,
PH7.8
Crystal Properties Matthews coefficient Solvent content 2.27 45.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.164 α = 90 b = 78.357 β = 101.62 c = 92.433 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 2022-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.965459 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 1.9 45.27 99.6 0.993 8 3.4 77039
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 1.9 1.94 0.775
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 1.9 42.24 73216 3801 99.55 0.17555 0.17406 0.1849 0.20415 0.2138 RANDOM 19.688
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] -0.33 -0.55 -0.8 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.972 r_dihedral_angle_4_deg 18.369 r_dihedral_angle_3_deg 14.481 r_dihedral_angle_1_deg 6.301 r_long_range_B_refined 5.381 r_long_range_B_other 5.346 r_scangle_other 4.027 r_mcangle_it 2.724 r_mcangle_other 2.724 r_scbond_it 2.545
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.972 r_dihedral_angle_4_deg 18.369 r_dihedral_angle_3_deg 14.481 r_dihedral_angle_1_deg 6.301 r_long_range_B_refined 5.381 r_long_range_B_other 5.346 r_scangle_other 4.027 r_mcangle_it 2.724 r_mcangle_other 2.724 r_scbond_it 2.545 r_scbond_other 2.545 r_mcbond_it 1.766 r_mcbond_other 1.765 r_angle_refined_deg 1.595 r_angle_other_deg 1.415 r_chiral_restr 0.207 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 7220 Nucleic Acid Atoms Solvent Atoms 485 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing