☰ Navigation Tabs
Co-structure of Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform and brain penetrant inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JPS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 303 RESERVOIR SOLUTION : 12%-20% PEG 3350, 0.125M-0.20M KSCN
PROTEIN SOLUTION : 20MM TRIS PH 7.2, 200MM NACL, 1% BETAINE,
1% ETHYLENE GLYCOL, 0.02% CHAPS, 5MM DTT,
PROTEIN IS 7.4 MG/ML
FORMATION METHOD : SOAKING
PROTOCOL : SET UP APO XTALS DROPS IN 1:1 RATIO IN 30C,
REMARK 280 XTALS GROW OVERNIGHT, THEN ADD 2MM OF STOCK CPD AND INCUBATE FOR A FEW HOURS METHOD : VAPOR DIFFUSION - HANGING DROP
TEMPERATURE : 303.0
CRYO PROTOCOL : 20% ETHYLENE GLYCOL PLUS WELL SOLUTION
Crystal Properties Matthews coefficient Solvent content 2.25 45.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.077 α = 90 b = 107.847 β = 90 c = 133.723 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 2016-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.000 ALS 5.0.2
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 2.3 83.95 99.8 0.075 0.079 0.023 0.999 15.9 12.7 64894
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 2.3 2.42 99 1.522 1.59 0.454 0.844 12
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 2.3 83.95 1.34 64537 3181 99.39 0.2423 0.2407 0.2388 0.2711 0.2675 Random
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.601 f_angle_d 0.386 f_chiral_restr 0.037 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9658 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing