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THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34 IN COMPLEX WITH 3-METHYLADENINE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X6H PDB ENTRY 2X6H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 PROTEIN WAS CRYSTALLISED IN 0.88M AMMONIUM SULPHATE, 100MM DI-POTASSIUM HYDROGEN PHOSPHATE AND 100MM DI-SODIUM HYDROGEN PHOSPHATE (TITRATED TO PH 7.5 WITH ORTHOPHOSPHORIC ACID). PROTEIN WAS SOAKED WITH 1MM 3-MA IN MOTHER LIQUOR.
Crystal Properties Matthews coefficient Solvent content 4.26 70.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.07 α = 90 b = 155.14 β = 90 c = 244.53 γ = 90
Symmetry Space Group I 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 ADSC QUANTUM 315r 2009-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 3.3 72.92 98.2 0.1 4.99 3.6 31665 1
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 3.3 3.48 99.7 0.69 1.04 3.66
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2X6H 3.3 61.13 30097 1564 97.5 0.245 0.242 0.293 0.3006 RANDOM 90.96
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] 2.94 2.09 -5.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.727 r_dihedral_angle_1_deg 25.474 r_dihedral_angle_3_deg 22.413 r_dihedral_angle_4_deg 19.064 r_scangle_it 1.859 r_mcangle_it 1.815 r_angle_refined_deg 1.647 r_mcbond_it 1.201 r_scbond_it 1.042 r_symmetry_vdw_refined 0.473
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.727 r_dihedral_angle_1_deg 25.474 r_dihedral_angle_3_deg 22.413 r_dihedral_angle_4_deg 19.064 r_scangle_it 1.859 r_mcangle_it 1.815 r_angle_refined_deg 1.647 r_mcbond_it 1.201 r_scbond_it 1.042 r_symmetry_vdw_refined 0.473 r_symmetry_hbond_refined 0.444 r_nbtor_refined 0.326 r_nbd_refined 0.3 r_xyhbond_nbd_refined 0.249 r_chiral_restr 0.1 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 8875 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing