3VOQ

Crystal structure of the pleckstrin homology domain of human Sin1, a TORC2 subunit


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ULBPDB entry 3ULB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1M Bis-Tris, 1.26M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.4464.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.293α = 90
b = 79.293β = 90
c = 123.599γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2010-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1241.531000.1058.62740927409
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.111000.9112.48.43907

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3ULB241.532740927346137099.950.1950.1950.19340.2239RANDOM34.6473
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]
-0.42-0.420.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.354
r_dihedral_angle_4_deg23.928
r_dihedral_angle_3_deg17.636
r_dihedral_angle_1_deg6.793
r_angle_refined_deg2.461
r_chiral_restr0.199
r_bond_refined_d0.027
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1805
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
BSSdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing