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Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) H91E mutant in complex with IP6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 Protein: 20mg/mL
IP6: 5mM
Precipitant condition: 26% PEG 6K
0.1M, NaOAc pH 5, 0.2M LiCl
Ratio: 1:1
Crystal Properties Matthews coefficient Solvent content 2.6 53.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.031 α = 90 b = 65.106 β = 90 c = 79.234 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 1.324 79.23 98.7 0.02 0.99 19.1 12.1 41338 17.2
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 1.324 1.35 0.265 0.85 2.2
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 1.324 50.303 41269 2087 98.654 0.178 0.1763 0.1844 0.2056 0.2126 20.096
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] -1.112 -0.479 1.591
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.183 r_dihedral_angle_3_deg 13.075 r_dihedral_angle_2_deg 10.577 r_lrange_it 8.848 r_lrange_other 8.84 r_dihedral_angle_1_deg 6.794 r_scangle_it 5.73 r_scangle_other 5.727 r_scbond_it 3.908 r_scbond_other 3.905
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.183 r_dihedral_angle_3_deg 13.075 r_dihedral_angle_2_deg 10.577 r_lrange_it 8.848 r_lrange_other 8.84 r_dihedral_angle_1_deg 6.794 r_scangle_it 5.73 r_scangle_other 5.727 r_scbond_it 3.908 r_scbond_other 3.905 r_mcangle_it 3.122 r_mcangle_other 3.12 r_angle_refined_deg 2.266 r_mcbond_it 2.125 r_mcbond_other 2.12 r_angle_other_deg 0.771 r_symmetry_nbd_refined 0.359 r_nbd_other 0.265 r_xyhbond_nbd_refined 0.254 r_symmetry_xyhbond_nbd_refined 0.236 r_nbd_refined 0.216 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.183 r_metal_ion_refined 0.165 r_chiral_restr 0.114 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_other 0.048 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1186 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 52
Software Software Software Name Purpose autoPROC data processing Aimless data scaling REFMAC refinement Coot model building REFMAC phasing autoPROC data reduction