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HumanDiphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) E108N mutant in complex with IP6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 Protein: 20mg/mL
IP6: 10mM
Precipitant condition: 25% PEG 3350, 0.1M Bis-Tris pH 5.5, 0.2M NaCl
Ratio: 1:2
Crystal Properties Matthews coefficient Solvent content 2.6 53.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.473 α = 90 b = 65.398 β = 90 c = 77.972 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 PILATUS 6M 2024-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 1.13 50.1 94.4 0.02 0.999 16.72 11.8 51069 13.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.13 1.23 0.38 0.67 1.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.13 50.1 51069 2564 76.255 0.175 0.1731 0.1797 0.2035 0.2077 15.848
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] 0.062 -0.076 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.467 r_dihedral_angle_3_deg 13.569 r_dihedral_angle_2_deg 10.583 r_lrange_it 7.24 r_lrange_other 7.026 r_dihedral_angle_1_deg 6.339 r_scangle_other 4.942 r_scangle_it 4.931 r_scbond_other 3.255 r_scbond_it 3.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.467 r_dihedral_angle_3_deg 13.569 r_dihedral_angle_2_deg 10.583 r_lrange_it 7.24 r_lrange_other 7.026 r_dihedral_angle_1_deg 6.339 r_scangle_other 4.942 r_scangle_it 4.931 r_scbond_other 3.255 r_scbond_it 3.211 r_mcangle_it 2.428 r_mcangle_other 2.426 r_angle_refined_deg 2.096 r_mcbond_it 1.633 r_mcbond_other 1.626 r_angle_other_deg 0.7 r_metal_ion_refined 0.424 r_nbd_refined 0.217 r_symmetry_nbd_refined 0.209 r_xyhbond_nbd_refined 0.194 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.182 r_nbd_other 0.176 r_symmetry_xyhbond_nbd_refined 0.173 r_chiral_restr 0.11 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1209 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 42
Software Software Software Name Purpose autoPROC data processing REFMAC refinement Coot model building autoPROC data reduction autoPROC data scaling REFMAC phasing