4NZM

Crystal structure of the catalytic domain of PPIP5K2 in complex with AMPPNP and 5-PA-InsP5


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727712% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM AMPPNP with 2 mM CdCl2 Soaking under 22% PEG3350, 10 mM MgCl2 0.1 M Sodium Acetate, pH5.2 with 10 mM 5PA-InsP5, 3 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7555.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.623α = 90
b = 111.226β = 90
c = 41.443γ = 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
125097.40.11417.44.928028280283
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)
122.0391.30.5113.231307

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 3T9B234.282613026130169896.560.200270.200270.198220.23145RANDOM23.063
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]
-0.031.12-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.531
r_dihedral_angle_4_deg15.365
r_dihedral_angle_3_deg14.112
r_long_range_B_refined6.407
r_long_range_B_other5.827
r_dihedral_angle_1_deg5.199
r_angle_other_deg3.583
r_scangle_other2.18
r_scbond_other1.471
r_scbond_it1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.531
r_dihedral_angle_4_deg15.365
r_dihedral_angle_3_deg14.112
r_long_range_B_refined6.407
r_long_range_B_other5.827
r_dihedral_angle_1_deg5.199
r_angle_other_deg3.583
r_scangle_other2.18
r_scbond_other1.471
r_scbond_it1.47
r_angle_refined_deg1.296
r_mcangle_it1.212
r_mcangle_other1.212
r_mcbond_it0.686
r_mcbond_other0.686
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_other0.005
r_gen_planes_refined0.004
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2604
Nucleic Acid Atoms
Solvent Atoms348
Heterogen Atoms74

Software

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