☰ Navigation Tabs
Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and 5-(PCF2P)-IP5, an analog of 5-IP7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T9D 3T9D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 14% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM AMPPNP, 2 mM CdCl2, Soaking with 2mM 5-PCF2P-InsP5 under pH 5.2 for 3 days , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.65 53.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.082 α = 90 b = 109.899 β = 90 c = 41.09 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 PIXEL DECTRIS EIGER X 16M 2020-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.75 50 99.1 0.087 0.096 0.04 11.3 5.4 40858
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 1.75 1.78 99.5 0.79 0.879 0.379 0.673 5.1
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 3T9D 1.75 38.52 38308 2023 98.04 0.1267 0.1241 0.1386 0.1752 0.1841 RANDOM 21.625
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] 0.89 1.1 -1.99
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 16.194 r_dihedral_angle_3_deg 14.735 r_dihedral_angle_2_deg 7.725 r_dihedral_angle_1_deg 6.098 r_angle_refined_deg 1.642 r_angle_other_deg 0.813 r_chiral_restr 0.133 r_bond_refined_d 0.011 r_gen_planes_other 0.011 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 16.194 r_dihedral_angle_3_deg 14.735 r_dihedral_angle_2_deg 7.725 r_dihedral_angle_1_deg 6.098 r_angle_refined_deg 1.642 r_angle_other_deg 0.813 r_chiral_restr 0.133 r_bond_refined_d 0.011 r_gen_planes_other 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2550 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 78
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing