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THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34 IN COMPLEX WITH PIK-93
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 0.5MM PIK-93 IN MOTHER LIQUOR.
Crystal Properties Matthews coefficient Solvent content 4.15 70.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.95 α = 90 b = 156.33 β = 90 c = 242.91 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 3.5 72.28 99.7 0.11 4.8 3.52 26700 1.2
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 3.5 3.69 99.9 0.45 1.18 3.64
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 2X6H 3.5 61.62 25387 1313 99.5 0.232 0.23 0.2248 0.272 0.2639 RANDOM 66.27
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] 0.36 3.02 -3.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.51 r_dihedral_angle_1_deg 25.4 r_dihedral_angle_3_deg 22.196 r_dihedral_angle_4_deg 18.957 r_scangle_it 2.049 r_angle_refined_deg 1.658 r_mcangle_it 1.258 r_scbond_it 1.128 r_mcbond_it 0.755 r_symmetry_vdw_refined 0.665
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.51 r_dihedral_angle_1_deg 25.4 r_dihedral_angle_3_deg 22.196 r_dihedral_angle_4_deg 18.957 r_scangle_it 2.049 r_angle_refined_deg 1.658 r_mcangle_it 1.258 r_scbond_it 1.128 r_mcbond_it 0.755 r_symmetry_vdw_refined 0.665 r_symmetry_hbond_refined 0.431 r_nbtor_refined 0.33 r_nbd_refined 0.295 r_xyhbond_nbd_refined 0.231 r_chiral_restr 0.11 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 8919 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing