4NZN

Crystal structure of the catalytic domain of PPIP5K2 in complex with AMPPNP and 2-O-BN-5-PA-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 Sodium Acetate, pH5.2 with 5 mM 2-O-Bn-5-PA-InsP4, 3 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7254.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.316α = 90
b = 110.69β = 90
c = 41.301γ = 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
11.755099.80.071285.742399423993
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)
11.751.7897.90.5312.54.82037

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 3T9B1.7533.123972039720261999.230.143340.143340.140960.17969RANDOM24.359
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]
0.33-0.09-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.679
r_dihedral_angle_2_deg36.447
r_dihedral_angle_4_deg13.021
r_dihedral_angle_3_deg11.716
r_sphericity_bonded10.132
r_long_range_B_refined5.427
r_dihedral_angle_1_deg5.328
r_long_range_B_other4.254
r_scangle_other3.467
r_scbond_it2.648
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.679
r_dihedral_angle_2_deg36.447
r_dihedral_angle_4_deg13.021
r_dihedral_angle_3_deg11.716
r_sphericity_bonded10.132
r_long_range_B_refined5.427
r_dihedral_angle_1_deg5.328
r_long_range_B_other4.254
r_scangle_other3.467
r_scbond_it2.648
r_scbond_other2.647
r_mcangle_it2.51
r_mcangle_other2.509
r_rigid_bond_restr2.464
r_mcbond_it2.015
r_mcbond_other1.919
r_angle_refined_deg1.381
r_angle_other_deg0.795
r_chiral_restr0.101
r_bond_refined_d0.006
r_gen_planes_refined0.004
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2604
Nucleic Acid Atoms
Solvent Atoms390
Heterogen Atoms76

Software

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