7N7M

Crystal Structure of PI5P4KIIAlpha complex with BI-2536


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YBX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52950.2 M Lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, 25% (w/v) Polyethylene glycol 3350
Crystal Properties
Matthews coefficientSolvent content
2.9658.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.411α = 90
b = 136.411β = 90
c = 95.006γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152015-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.979APS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.64097.50.0820.0870.027129.616167
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)
12.62.69910.8270.9070.3560.7085.7

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 REPLACEMENTTHROUGHOUT2YBX2.6401542274597.490.19730.19540.2357RANDOM69.628
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]
0.860.430.86-2.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.362
r_dihedral_angle_4_deg18.446
r_dihedral_angle_3_deg17.448
r_dihedral_angle_1_deg5.672
r_angle_refined_deg1.228
r_chiral_restr0.083
r_bond_refined_d0.008
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2367
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms53

Software

Software
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACphasing