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Inhibition of Human Menin by VTP-50469
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GPQ PDB entry 4GPQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 14%(w/v) PEG3350
0.2M Potassium thiocyanate
0.1M MES pH=6.0
15%(v/v) Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.34 47.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.97 α = 90 b = 86.08 β = 90 c = 202.04 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 PILATUS 6M Mirrors 2016-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1. APS 17-ID
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 1.9 58.97 99.9 0.052 19.9 6.4 81943
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 1.9 1.949 99.97 0.3 4.7
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 PDB entry 4GPQ 1.9 48.65 77796 4146 99.93 0.17036 0.16848 0.1789 0.20642 0.2155 RANDOM 29.434
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] -0.02 -0.03 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.293 r_dihedral_angle_4_deg 20.107 r_dihedral_angle_3_deg 15.765 r_long_range_B_refined 8.173 r_long_range_B_other 8.138 r_dihedral_angle_1_deg 6.682 r_scangle_other 6.014 r_mcangle_it 4.45 r_mcangle_other 4.45 r_scbond_it 3.882
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.293 r_dihedral_angle_4_deg 20.107 r_dihedral_angle_3_deg 15.765 r_long_range_B_refined 8.173 r_long_range_B_other 8.138 r_dihedral_angle_1_deg 6.682 r_scangle_other 6.014 r_mcangle_it 4.45 r_mcangle_other 4.45 r_scbond_it 3.882 r_scbond_other 3.881 r_mcbond_it 3.088 r_mcbond_other 3.087 r_angle_refined_deg 2.006 r_angle_other_deg 1.547 r_chiral_restr 0.121 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.009 r_gen_planes_other 0.008 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 7310 Nucleic Acid Atoms Solvent Atoms 572 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing