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Crystal structure of VPS34 in complex with inhibitor SB02024
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LS8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 22.5 % PEG3350, 0.2 M ammonium acetate, 0.1 M HEPES pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.6 65.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 288.824 α = 90 b = 98.65 β = 92.266 c = 62.895 γ = 90
Symmetry Space Group C 1 2 1
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 TOROIDAL MIRROR 2015-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97802 ESRF ID29
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 2.06 49.374 99.6 0.055 0.07 0.043 0.999 12.6 4.5 108408
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 2.06 2.13 99.3 0.9 1.164 0.73 0.53 1.4 4.4
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 FREE R-VALUE 2.06 49.374 108391 5315 99.481 0.184 0.1816 0.1899 0.2245 0.2321 47.699
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] -0.131 -1.143 -0.735 0.953
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.943 r_dihedral_angle_3_deg 12.685 r_lrange_it 7.322 r_lrange_other 7.322 r_dihedral_angle_2_deg 6.213 r_scangle_it 5.924 r_scangle_other 5.924 r_dihedral_angle_1_deg 5.694 r_mcangle_it 3.867 r_mcangle_other 3.866
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.943 r_dihedral_angle_3_deg 12.685 r_lrange_it 7.322 r_lrange_other 7.322 r_dihedral_angle_2_deg 6.213 r_scangle_it 5.924 r_scangle_other 5.924 r_dihedral_angle_1_deg 5.694 r_mcangle_it 3.867 r_mcangle_other 3.866 r_scbond_it 3.798 r_scbond_other 3.798 r_mcbond_it 2.731 r_mcbond_other 2.731 r_angle_refined_deg 1.315 r_angle_other_deg 0.467 r_nbd_refined 0.215 r_nbd_other 0.191 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.141 r_symmetry_nbd_refined 0.121 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.065 r_gen_planes_refined 0.005 r_bond_refined_d 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 8728 Nucleic Acid Atoms Solvent Atoms 590 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing