4D0M

Phosphatidylinositol 4-kinase III beta in a complex with Rab11a-GTP- gamma-S and the Rab-binding domain of FIP3


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
116% PEG 6K, 0.01 M NA CITRATE
Crystal Properties
Matthews coefficientSolvent content
2.958

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 199.504α = 90
b = 134.465β = 90.33
c = 294.328γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2014-02-09MSINGLE 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
1649.8895.90.1717.85.637822
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)
166.27971.032.25.2

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 4D0L6294.3235405192594.330.258880.25330.35946RANDOM261.052
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]
-11.354.490.6910.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.468
r_dihedral_angle_3_deg17.225
r_dihedral_angle_4_deg16.46
r_dihedral_angle_1_deg6.433
r_angle_refined_deg1.366
r_angle_other_deg1.016
r_symmetry_hbond_refined0.899
r_symmetry_vdw_refined0.711
r_symmetry_hbond_other0.594
r_symmetry_vdw_other0.571
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.468
r_dihedral_angle_3_deg17.225
r_dihedral_angle_4_deg16.46
r_dihedral_angle_1_deg6.433
r_angle_refined_deg1.366
r_angle_other_deg1.016
r_symmetry_hbond_refined0.899
r_symmetry_vdw_refined0.711
r_symmetry_hbond_other0.594
r_symmetry_vdw_other0.571
r_xyhbond_nbd_other0.342
r_metal_ion_refined0.33
r_xyhbond_nbd_refined0.299
r_nbd_refined0.239
r_nbd_other0.188
r_nbtor_refined0.177
r_nbtor_other0.084
r_chiral_restr0.071
r_bond_refined_d0.012
r_bond_other_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.005
r_metal_ion_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms65286
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms684

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing