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Crystal structure of VPS34 in complex with (2S)-8-((3R)-3- Methylmorpholin-4-yl)-1-(3-methyl-2-oxo- butyl)-2-(trifluoromethyl)-3, 4-dihydro-2H-pyrimido(1,2-a)pyrimidin-6- one, processed with the CrystalDirect automated mounting and cryo-cooling technology
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M TRIS, PH=7.5, 1.8 M AMMONIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 2.88 57.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.215 α = 90 b = 145.763 β = 90 c = 61.474 γ = 90
Symmetry Space Group P 21 21 2
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 ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.7 30 99.9 0.14 5.1 22467 2.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.85 100 2.1 5.1
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 OTHER THROUGHOUT NONE 2.7 30 21323 1108 99.84 0.20839 0.20534 0.2111 0.26667 0.2647 RANDOM 45.423
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] 6.19 -0.01 -6.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.657 r_dihedral_angle_4_deg 18.737 r_dihedral_angle_3_deg 16.523 r_dihedral_angle_1_deg 5.861 r_mcangle_it 4.584 r_scbond_it 3.321 r_mcbond_it 2.902 r_mcbond_other 2.901 r_angle_refined_deg 1.527 r_angle_other_deg 0.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.657 r_dihedral_angle_4_deg 18.737 r_dihedral_angle_3_deg 16.523 r_dihedral_angle_1_deg 5.861 r_mcangle_it 4.584 r_scbond_it 3.321 r_mcbond_it 2.902 r_mcbond_other 2.901 r_angle_refined_deg 1.527 r_angle_other_deg 0.816 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4304 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement