4D0L

Phosphatidylinositol 4-kinase III beta-PIK93 in a complex with Rab11a- GTP gammaS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IHYPDB ENTRIES 3IHY AND 1OIW
experimental modelPDB 1OIWPDB ENTRIES 3IHY AND 1OIW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.615% (W/V) PEG 4000, 0.1 M NA CITRATE PH 5.6, AND 0.2 M AMMONIUM ACETATE
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.795α = 90
b = 146.925β = 90
c = 188.335γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2013-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
12.848.5199.90.1110.94.270875
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)
12.82.8699.91.041.14.3

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 ENTRIES 3IHY AND 1OIW2.94115.8458056309599.540.218430.216260.2594RANDOM69.221
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]
60.74-6.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.023
r_dihedral_angle_3_deg18.591
r_dihedral_angle_4_deg17.473
r_scangle_it7.139
r_mcangle_it6.6
r_dihedral_angle_1_deg6.459
r_scbond_it4.434
r_mcbond_it4.172
r_mcbond_other4.172
r_angle_refined_deg1.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.023
r_dihedral_angle_3_deg18.591
r_dihedral_angle_4_deg17.473
r_scangle_it7.139
r_mcangle_it6.6
r_dihedral_angle_1_deg6.459
r_scbond_it4.434
r_mcbond_it4.172
r_mcbond_other4.172
r_angle_refined_deg1.49
r_angle_other_deg1.225
r_metal_ion_refined0.305
r_xyhbond_nbd_other0.304
r_symmetry_hbond_refined0.298
r_xyhbond_nbd_refined0.252
r_nbd_refined0.248
r_symmetry_vdw_refined0.243
r_symmetry_vdw_other0.236
r_nbd_other0.213
r_nbtor_refined0.191
r_nbtor_other0.091
r_chiral_restr0.081
r_symmetry_hbond_other0.053
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.005
r_metal_ion_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms15675
Nucleic Acid Atoms
Solvent Atoms18
Heterogen Atoms171

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing