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Inhibition of Human Menin by SNDX-5613
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PKC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.9 294 0.1M HEPES pH 7.9, 24%(w/v) PEG 3350, 0.2M Magnesium nitrate, 20%(v/v) Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.26 45.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.417 α = 90 b = 86.134 β = 90 c = 202.027 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 X 16M 2021-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953644 Australian Synchrotron MX2
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 1.85 48.39 99.93 0.121 0.163 0.116 0.994 6.2 3.8 87900 37.82
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 1.85 1.898 99.97 1.43 1.67 1.13 0.27 0.8 3.4
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 (All) 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 FREE R-VALUE 6PKC 1.85 48.3 87900 4385 99.932 0.174 0.174 0.1726 0.1824 0.2098 0.2169 Random 29.349
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] 0.002 -0.001 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.526 r_dihedral_angle_4_deg 15.546 r_dihedral_angle_3_deg 14.202 r_dihedral_angle_1_deg 9.016 r_lrange_it 6.506 r_lrange_other 6.462 r_scangle_it 5.17 r_scangle_other 5.17 r_mcangle_it 3.606 r_mcangle_other 3.605
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.526 r_dihedral_angle_4_deg 15.546 r_dihedral_angle_3_deg 14.202 r_dihedral_angle_1_deg 9.016 r_lrange_it 6.506 r_lrange_other 6.462 r_scangle_it 5.17 r_scangle_other 5.17 r_mcangle_it 3.606 r_mcangle_other 3.605 r_scbond_it 3.425 r_scbond_other 3.425 r_mcbond_it 2.566 r_mcbond_other 2.565 r_angle_refined_deg 1.598 r_chiral_restr_other 1.564 r_angle_other_deg 1.513 r_nbd_refined 0.232 r_xyhbond_nbd_other 0.195 r_nbd_other 0.19 r_xyhbond_nbd_refined 0.183 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.167 r_symmetry_nbd_refined 0.166 r_symmetry_xyhbond_nbd_other 0.122 r_ncsr_local_group_1 0.101 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7282 Nucleic Acid Atoms Solvent Atoms 520 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling PHASER phasing