☰ Navigation Tabs
Menin in complex with Ziftomenib (KO-539)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GPQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Crystal Properties Matthews coefficient Solvent content 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.395 α = 90 b = 80.181 β = 90 c = 124.924 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 CCD MARMOSAIC 300 mm CCD 2016-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.57 50 100 0.072 33.4 6.9 68768
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.57 1.6 100 0.772 2.13 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.57 41.467 68695 3434 99.952 0.16 0.1581 0.1592 0.1933 0.1941 23.252
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] 1.513 0.053 -1.566
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.077 r_dihedral_angle_3_deg 12.183 r_dihedral_angle_2_deg 9.052 r_lrange_it 6.978 r_lrange_other 6.977 r_dihedral_angle_1_deg 6.13 r_scangle_it 5.536 r_scangle_other 5.535 r_dihedral_angle_other_2_deg 4.733 r_scbond_it 3.729
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.077 r_dihedral_angle_3_deg 12.183 r_dihedral_angle_2_deg 9.052 r_lrange_it 6.978 r_lrange_other 6.977 r_dihedral_angle_1_deg 6.13 r_scangle_it 5.536 r_scangle_other 5.535 r_dihedral_angle_other_2_deg 4.733 r_scbond_it 3.729 r_scbond_other 3.728 r_mcangle_other 3.663 r_mcangle_it 3.662 r_mcbond_it 2.467 r_mcbond_other 2.467 r_angle_refined_deg 1.825 r_angle_other_deg 0.648 r_symmetry_xyhbond_nbd_refined 0.279 r_symmetry_nbd_refined 0.239 r_nbd_refined 0.222 r_nbd_other 0.186 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_chiral_restr_other 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3670 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing