4NZO

Crystal structure of the catalytic domain of PPIP5K2 in complex with AMPPNP and 2,5-DI-O-BN-INSP4


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 HEPES, pH7.0 with 10 mM 2, 5-di-O-Bn-InsP4, 3 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7254.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.11α = 90
b = 111.133β = 90
c = 41.299γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

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
11.95099.90.07329.37.233324333243
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)
11.91.9399.60.463.76.41612

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 3T9B1.935.533122831228203699.580.18120.18120.1790.21542RANDOM27.166
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]
0.64-0.25-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.386
r_dihedral_angle_4_deg15.108
r_dihedral_angle_3_deg13.774
r_long_range_B_refined7.215
r_long_range_B_other6.964
r_dihedral_angle_1_deg5.554
r_scangle_other3.716
r_angle_other_deg3.541
r_mcangle_it3.001
r_mcangle_other3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.386
r_dihedral_angle_4_deg15.108
r_dihedral_angle_3_deg13.774
r_long_range_B_refined7.215
r_long_range_B_other6.964
r_dihedral_angle_1_deg5.554
r_scangle_other3.716
r_angle_other_deg3.541
r_mcangle_it3.001
r_mcangle_other3
r_scbond_it2.348
r_scbond_other2.347
r_mcbond_it1.823
r_mcbond_other1.823
r_angle_refined_deg1.545
r_chiral_restr0.094
r_bond_refined_d0.01
r_gen_planes_other0.009
r_gen_planes_refined0.006
r_bond_other_d
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 Atoms2604
Nucleic Acid Atoms
Solvent Atoms342
Heterogen Atoms76

Software

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