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Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) H91E mutant in complex with 1,5-(PCP)-IP5 (PCP-IP8)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 Protein: 20mg/mL
PCP-IP8: 10mM
Precipitant condition: 26% PEG 6K, 0.1M NaOAc pH 5, 0.2M LiCl, 1mM MnCl2
Ratio: 1:1
Crystal Properties Matthews coefficient Solvent content 2.6 53.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.423 α = 90 b = 65.359 β = 90 c = 78.094 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 2022-03-12 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 1.21 50.121 91.3 0.024 0.997 15.8 12.3 42464 15.5
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 1.21 1.3 0.47 0.451 1.4
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 1.213 50.121 42464 2128 78.318 0.164 0.1631 0.1724 0.1887 0.1915 18.856
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] -0.09 0.002 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.699 r_dihedral_angle_3_deg 13.244 r_lrange_it 10.48 r_dihedral_angle_2_deg 9.792 r_lrange_other 9.546 r_dihedral_angle_1_deg 6.832 r_scangle_it 5.8 r_scangle_other 5.703 r_scbond_it 3.678 r_scbond_other 3.608
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.699 r_dihedral_angle_3_deg 13.244 r_lrange_it 10.48 r_dihedral_angle_2_deg 9.792 r_lrange_other 9.546 r_dihedral_angle_1_deg 6.832 r_scangle_it 5.8 r_scangle_other 5.703 r_scbond_it 3.678 r_scbond_other 3.608 r_mcangle_it 3.024 r_mcangle_other 3.022 r_angle_refined_deg 2.105 r_mcbond_it 2.012 r_mcbond_other 2.011 r_angle_other_deg 0.704 r_nbd_refined 0.258 r_symmetry_nbd_refined 0.233 r_xyhbond_nbd_refined 0.215 r_symmetry_xyhbond_nbd_refined 0.213 r_symmetry_nbd_other 0.198 r_nbd_other 0.19 r_nbtor_refined 0.18 r_chiral_restr 0.106 r_symmetry_xyhbond_nbd_other 0.088 r_symmetry_nbtor_other 0.085 r_metal_ion_refined 0.055 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1186 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 56
Software Software Software Name Purpose autoPROC data processing REFMAC refinement Coot model building autoPROC data reduction autoPROC data scaling REFMAC phasing