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Wild-type Menin complexed with DSP-5336
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 18%(w/v) PEG3350, 0.2M POTASIUM THIOCYANATE, 0.1 M MES PH=6.0, 20%(v/v) ETHYLENE GLYCOL,
PH 6.0
Crystal Properties Matthews coefficient Solvent content 2.3 46.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.429 α = 90 b = 78.553 β = 101.64 c = 93.007 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 2022-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95374 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 1.5 45.55 100 0.997 11.5 6.9 158545
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 1.5 1.53 0.716
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 1.5 42.41 150358 8145 99.95 0.18595 0.18441 0.1913 0.2138 0.2179 RANDOM 16.408
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] 0.03 -0.36 -0.23 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.27 r_dihedral_angle_4_deg 16.755 r_dihedral_angle_3_deg 14.086 r_dihedral_angle_1_deg 6.032 r_long_range_B_refined 4.883 r_long_range_B_other 4.796 r_scangle_other 3.861 r_scbond_it 2.505 r_scbond_other 2.505 r_mcangle_it 2.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.27 r_dihedral_angle_4_deg 16.755 r_dihedral_angle_3_deg 14.086 r_dihedral_angle_1_deg 6.032 r_long_range_B_refined 4.883 r_long_range_B_other 4.796 r_scangle_other 3.861 r_scbond_it 2.505 r_scbond_other 2.505 r_mcangle_it 2.35 r_mcangle_other 2.35 r_angle_refined_deg 1.787 r_mcbond_it 1.574 r_mcbond_other 1.574 r_angle_other_deg 1.555 r_chiral_restr 0.324 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 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 721 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing