5E3U

Crystal structure of phosphatidylinositol-4-phosphate 5-kinase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277peg
Crystal Properties
Matthews coefficientSolvent content
3.5871.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.134α = 90
b = 88.134β = 90
c = 155.757γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152014-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.987NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.6401005.513.676557655

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT3.640723837599.880.20360.20060.2607RANDOM78.749
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]
3.013.01-6.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.375
r_dihedral_angle_3_deg22.118
r_dihedral_angle_4_deg20.223
r_mcangle_it8.96
r_dihedral_angle_1_deg8.034
r_mcbond_other5.451
r_mcbond_it5.45
r_angle_refined_deg1.603
r_angle_other_deg0.861
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.375
r_dihedral_angle_3_deg22.118
r_dihedral_angle_4_deg20.223
r_mcangle_it8.96
r_dihedral_angle_1_deg8.034
r_mcbond_other5.451
r_mcbond_it5.45
r_angle_refined_deg1.603
r_angle_other_deg0.861
r_chiral_restr0.078
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2268
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
Cootmodel building