3T7A

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP at pH 5.2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3T54PDB ENTRY 3T54

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727712% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, 1 mM ATP, 2 mM CdCl2 Soaking under pH5.2 overnight , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7154.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.973α = 90
b = 110.807β = 90
c = 41.381γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-02-09MSINGLE 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
11.75099.20.05728.55.345377-3
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)
11.71.7394.80.42334

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 3T541.741.2842377280298.720.180950.180950.179270.20635Equivalent and expanded17.327
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]
0.5-0.34-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.997
r_dihedral_angle_4_deg14.301
r_dihedral_angle_3_deg11.293
r_dihedral_angle_1_deg5.429
r_scangle_it3.498
r_scbond_it2.066
r_mcangle_it1.376
r_angle_refined_deg1.189
r_mcbond_it0.719
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.997
r_dihedral_angle_4_deg14.301
r_dihedral_angle_3_deg11.293
r_dihedral_angle_1_deg5.429
r_scangle_it3.498
r_scbond_it2.066
r_mcangle_it1.376
r_angle_refined_deg1.189
r_mcbond_it0.719
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2558
Nucleic Acid Atoms
Solvent Atoms431
Heterogen Atoms62

Software

Software
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing