8A5X

Crystal structure of phosphatidyl inositol 4-kinase II beta in complex with MM1373


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WTV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29110% w/v PEG 8.000, 20% v/v ethylene glycol, 3% v/v DMSO, 100 mM bicine/Trizma base pH 8.5, 20 mM 1,6-hexanediol, 20 mM 1-butanol, 20 mM 1,2-propanediol, 20 mM 2-propanol, 20 mM 1,4-butanediol, 20 mM 1,3-propanediol
Crystal Properties
Matthews coefficientSolvent content
2.4148.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.383α = 90
b = 87.007β = 107.78
c = 71.376γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200K2022-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54187

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.431.6392.170.099530.11640.059960.99613.383.62041032.31
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.48684.380.60790.70590.35780.7642.293.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4WTV2.431.631.3420402102092.230.21150.21050.231random selection43.98
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d10.8776
f_angle_d0.477
f_chiral_restr0.0402
f_plane_restr0.0039
f_bond_d0.0022
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3781
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms22

Software

Software
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement