4O4E

Crystal Structure of an Inositol hexakisphosphate kinase EhIP6KA in complexed with ATP and Ins(1,3,4,5,6)P5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4O4CPDB Entry 4O4C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.22770.4 M NaH2PO4 in the presence of 10 mM ATP,5 mM IP3, 20 mM MgCl2. The crystals were further soaked under 22% (w/v) PEG 3350, 10 mM MgCl2, 10 mM ATP, 0.1 M sodium acetate, pH 5.2, 10 mM IP5 for 3 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5150.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.999α = 90
b = 102.999β = 90
c = 110.976γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.95099.30.04942.98.123544235443
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9393.90.5272.66.31111

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB Entry 4O4C1.928.862226522265118998.720.185050.185050.183280.21926RANDOM32.688
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]
-0.79-0.791.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.085
r_dihedral_angle_3_deg14.243
r_dihedral_angle_4_deg13.488
r_long_range_B_refined7.438
r_long_range_B_other7.251
r_dihedral_angle_1_deg6.625
r_scangle_other3.743
r_mcangle_it2.903
r_mcangle_other2.902
r_scbond_it2.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.085
r_dihedral_angle_3_deg14.243
r_dihedral_angle_4_deg13.488
r_long_range_B_refined7.438
r_long_range_B_other7.251
r_dihedral_angle_1_deg6.625
r_scangle_other3.743
r_mcangle_it2.903
r_mcangle_other2.902
r_scbond_it2.307
r_scbond_other2.29
r_mcbond_it1.79
r_mcbond_other1.789
r_angle_refined_deg1.729
r_angle_other_deg0.838
r_chiral_restr0.133
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2046
Nucleic Acid Atoms
Solvent Atoms195
Heterogen Atoms70

Software

Software
Software NamePurpose
HKL-2000data collection
CCP4model building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing