2X6J

THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34 IN COMPLEX WITH PIK-93


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2X6HPDB ENTRY 2X6H

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). PROTEIN WAS SOAKED WITH 0.5MM PIK-93 IN MOTHER LIQUOR.
Crystal Properties
Matthews coefficientSolvent content
4.1570.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.95α = 90
b = 156.33β = 90
c = 242.91γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
13.572.2899.70.114.83.52267001.2
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)
13.53.6999.90.451.183.64

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 2X6H3.561.6225387131399.50.2320.230.272RANDOM66.27
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]
0.363.02-3.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.51
r_dihedral_angle_1_deg25.4
r_dihedral_angle_3_deg22.196
r_dihedral_angle_4_deg18.957
r_scangle_it2.049
r_angle_refined_deg1.658
r_mcangle_it1.258
r_scbond_it1.128
r_mcbond_it0.755
r_symmetry_vdw_refined0.665
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.51
r_dihedral_angle_1_deg25.4
r_dihedral_angle_3_deg22.196
r_dihedral_angle_4_deg18.957
r_scangle_it2.049
r_angle_refined_deg1.658
r_mcangle_it1.258
r_scbond_it1.128
r_mcbond_it0.755
r_symmetry_vdw_refined0.665
r_symmetry_hbond_refined0.431
r_nbtor_refined0.33
r_nbd_refined0.295
r_xyhbond_nbd_refined0.231
r_chiral_restr0.11
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 Atoms8919
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing