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Crystal structure of the pleckstrin homology domain of human Sin1, a TORC2 subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ULB PDB entry 3ULB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M Bis-Tris, 1.26M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.44 64.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.293 α = 90 b = 79.293 β = 90 c = 123.599 γ = 90
Symmetry Space Group P 43 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 RAYONIX MX225HE 2010-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 41.53 100 0.105 8.6 27409 27409
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 2 2.11 100 0.911 2.4 8.4 3907
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3ULB 2 41.53 27409 27346 1370 99.95 0.195 0.195 0.1934 0.1919 0.2239 0.2223 RANDOM 34.6473
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] -0.42 -0.42 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.354 r_dihedral_angle_4_deg 23.928 r_dihedral_angle_3_deg 17.636 r_dihedral_angle_1_deg 6.793 r_angle_refined_deg 2.461 r_chiral_restr 0.199 r_bond_refined_d 0.027 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1805 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction BSS data collection MOSFLM data reduction SCALA data scaling MOLREP phasing