2X6K | pdb_00002x6k

THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34 IN COMPLEX WITH PI-103


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 PI-103 IN MOTHER LIQUOR.
Crystal Properties
Matthews coefficientSolvent content
4.1770.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.44α = 90
b = 155.68β = 90
c = 244γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-08-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.8777.8499.70.16.463.56270691.3
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)
13.53.691000.541.333.64

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2X6H3.561.7425729134099.50.2380.2350.230.2960.29RANDOM75.26
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]
3.192.13-5.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.739
r_dihedral_angle_1_deg25.182
r_dihedral_angle_3_deg23.104
r_dihedral_angle_4_deg16.918
r_scangle_it1.72
r_angle_refined_deg1.66
r_mcangle_it1.448
r_scbond_it0.953
r_mcbond_it0.894
r_symmetry_vdw_refined0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.739
r_dihedral_angle_1_deg25.182
r_dihedral_angle_3_deg23.104
r_dihedral_angle_4_deg16.918
r_scangle_it1.72
r_angle_refined_deg1.66
r_mcangle_it1.448
r_scbond_it0.953
r_mcbond_it0.894
r_symmetry_vdw_refined0.72
r_symmetry_hbond_refined0.468
r_nbtor_refined0.323
r_nbd_refined0.28
r_xyhbond_nbd_refined0.232
r_chiral_restr0.103
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 Atoms8995
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing