2X6H | pdb_00002x6h

THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E8XPDB ENTRY 1E8X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5PROTEIN 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).
Crystal Properties
Matthews coefficientSolvent content
4.1670.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.6α = 90
b = 154.79β = 90
c = 243.08γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.5772.3695.80.15.773.39445620.9
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)
12.93.0684.50.880.862.86

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1E8X2.972.3642331222895.70.2420.240.240.2780.27RANDOM40.39
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]
-2.813.96-1.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.598
r_dihedral_angle_1_deg25.632
r_dihedral_angle_3_deg22.692
r_dihedral_angle_4_deg19.708
r_scangle_it2.256
r_angle_refined_deg1.656
r_scbond_it1.265
r_mcangle_it0.961
r_symmetry_vdw_refined0.723
r_symmetry_hbond_refined0.686
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.598
r_dihedral_angle_1_deg25.632
r_dihedral_angle_3_deg22.692
r_dihedral_angle_4_deg19.708
r_scangle_it2.256
r_angle_refined_deg1.656
r_scbond_it1.265
r_mcangle_it0.961
r_symmetry_vdw_refined0.723
r_symmetry_hbond_refined0.686
r_mcbond_it0.489
r_nbtor_refined0.329
r_nbd_refined0.286
r_xyhbond_nbd_refined0.261
r_chiral_restr0.109
r_bond_refined_d0.011
r_gen_planes_refined0.009
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 AtomsNumber
Protein Atoms8886
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
BALBESphasing