4HN2

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP and a substrate analog 5PA-IP5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3T9BPDB entry 3T9B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP27712% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES pH 7.0, 1 mM AMPPNP, 2 mM CdCl2. Soaking with 2 mM 5-PA-InsP5 under pH 5.2 for 3 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7555.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.666α = 90
b = 110.768β = 90
c = 41.536γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2012-02-23MSINGLE 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
11.95098.30.07324.75.63309133091-3
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)
11.91.931000.3863.45.11614

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 3T9B1.933.2330868201197.80.193050.191170.22157Equivalent and expanded30.47
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]
0.65-0.22-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.154
r_dihedral_angle_4_deg15.052
r_dihedral_angle_3_deg12.68
r_dihedral_angle_1_deg5.179
r_scangle_it3.489
r_scbond_it2.052
r_mcangle_it1.399
r_angle_refined_deg1.249
r_mcbond_it0.713
r_chiral_restr0.082
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.154
r_dihedral_angle_4_deg15.052
r_dihedral_angle_3_deg12.68
r_dihedral_angle_1_deg5.179
r_scangle_it3.489
r_scbond_it2.052
r_mcangle_it1.399
r_angle_refined_deg1.249
r_mcbond_it0.713
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2604
Nucleic Acid Atoms
Solvent Atoms330
Heterogen Atoms74

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing