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Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and 1,5-(PA)2-IP4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM ATP and 2 mM CdCl2. The crystals were transferred to a stabilizing buffer containing 22% (w/v) PEG 3350, 10 mM MgCl2, 0.1 M sodium acetate, pH 5.2 at 4 oC overnight, while ATP in the crystals was hydrolyzed to ADP. The crystals were soaked under the above stabilizing buffer for three days with 2 mM analog.
Crystal Properties Matthews coefficient Solvent content 2.81 56.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.807 α = 90 b = 110.411 β = 90 c = 41.423 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2015-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.3 50 99.2 0.114 0.128 0.057 6 4.7 18773
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 95.5 0.438 0.49 0.215 0.89 4.7 865
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 3T7A 2.3 35.57 17585 1143 98.92 0.19287 0.18935 0.1893 0.24638 0.2468 RANDOM 22.434
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] 1 -0.32 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.103 r_dihedral_angle_3_deg 14.636 r_dihedral_angle_4_deg 12.632 r_long_range_B_refined 6.811 r_dihedral_angle_1_deg 5.752 r_mcangle_it 3.129 r_scbond_it 1.783 r_mcbond_it 1.761 r_angle_refined_deg 1.738 r_chiral_restr 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.103 r_dihedral_angle_3_deg 14.636 r_dihedral_angle_4_deg 12.632 r_long_range_B_refined 6.811 r_dihedral_angle_1_deg 5.752 r_mcangle_it 3.129 r_scbond_it 1.783 r_mcbond_it 1.761 r_angle_refined_deg 1.738 r_chiral_restr 0.133 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2539 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling PDB_EXTRACT data extraction XDS data scaling PHASER phasing