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Crystal structure of menin in complex with inhibitor compound 15
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OG3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% PEG 3350, 0.1M HEPES pH6.9, 0.2M Na Thiocyanate, 1% Tacsimate, 4% Isopropanol
Crystal Properties Matthews coefficient Solvent content 2.14 42.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.831 α = 90 b = 87.764 β = 90 c = 195.425 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 R 4M 2021-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 24.43 99.5 0.134 0.148 0.061 0.994 6.8 5.3 77476 24.97
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 98.6 0.624 0.71 0.332 0.338 2 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 24.43 1.41 77420 2000 99.38 0.1977 0.1965 0.1969 0.2436 0.2447 33.78
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.2869 f_angle_d 0.853 f_chiral_restr 0.0489 f_plane_restr 0.0078 f_bond_d 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7398 Nucleic Acid Atoms Solvent Atoms 721 Heterogen Atoms 72
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction Aimless data scaling PHASER phasing