3LJU

Crystal structure of full length centaurin alpha-1 bound with the head group of PIP3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FEHpdb entry 3FEH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29120% PEG3350, 0.2M ammonium chloride. Protein buffer: 0.02M HEPES pH 7.3, 0.3M sodium chloride, 0.001M TCEP, 5% glyccerol, 2.0mg/mL L-alpha-Phosphatidyl-D-myo-inositol 3,4,5-triphosphate, dioctanoyl, from SIGMA, catalog no. P9953, vapor diffusion, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.550.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.727α = 90
b = 66.414β = 90
c = 127.219γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97918APS19-ID

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
11.75098.80.1089.14.348266
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)
1.71.7397.30.4762.82338

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 3FEH1.7022048202243798.7140.1930.1910.231RANDOM13.169
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]
-0.7670.1760.591
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.748
r_dihedral_angle_3_deg12.401
r_dihedral_angle_4_deg12.148
r_dihedral_angle_1_deg6.067
r_scangle_it4.585
r_mcangle_it3.537
r_scbond_it3.058
r_mcbond_it2.414
r_angle_refined_deg1.474
r_angle_other_deg0.862
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.748
r_dihedral_angle_3_deg12.401
r_dihedral_angle_4_deg12.148
r_dihedral_angle_1_deg6.067
r_scangle_it4.585
r_mcangle_it3.537
r_scbond_it3.058
r_mcbond_it2.414
r_angle_refined_deg1.474
r_angle_other_deg0.862
r_mcbond_other0.816
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3036
Nucleic Acid Atoms
Solvent Atoms294
Heterogen Atoms53

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction