2IF8

Crystal structure of Inositol Phosphate Multikinase Ipk2 in complex with ADP and Mn2+ from S. cerevisiae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IEWPDB Entry: 2IEW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.7293100mM HEPES pH7.7, 200mM CaCl2, 28% PEG400 50mM ATP and 50 mM MnCl soaked, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9858.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 184.996α = 90
b = 184.996β = 90
c = 49.998γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A0.979NSLSX4A

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
12.4300.08811.62.836366
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)
12.3982.460.5691.62.4

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: 2IEW2.43036366192298.520.195340.192670.24593RANDOM47.898
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]
1.520.761.52-2.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.946
r_dihedral_angle_4_deg19.049
r_dihedral_angle_3_deg18.757
r_dihedral_angle_1_deg6.888
r_scangle_it3.067
r_scbond_it1.923
r_angle_refined_deg1.465
r_mcangle_it1.461
r_mcbond_it0.808
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.946
r_dihedral_angle_4_deg19.049
r_dihedral_angle_3_deg18.757
r_dihedral_angle_1_deg6.888
r_scangle_it3.067
r_scbond_it1.923
r_angle_refined_deg1.465
r_mcangle_it1.461
r_mcbond_it0.808
r_nbtor_refined0.304
r_symmetry_hbond_refined0.242
r_symmetry_vdw_refined0.23
r_xyhbond_nbd_refined0.218
r_nbd_refined0.21
r_chiral_restr0.095
r_symmetry_metal_ion_refined0.028
r_metal_ion_refined0.027
r_bond_refined_d0.013
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4174
Nucleic Acid Atoms
Solvent Atoms365
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing