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Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) H91M mutant in complex with IP6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 Protein: 19.5mg/mL
IP6: 10mM
Precipitant condition: 32% PEG 6K, 0.1M NaOAc pH 5, 0.2M LiCl, 1mM MgCl2
Ratio: 1:1
Crystal Properties Matthews coefficient Solvent content 2.6 53.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.412 α = 90 b = 64.869 β = 90 c = 78.644 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 2023-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.88560 ESRF ID23-1
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 1.39 39.35 94.4 0.05 0.99 9.5 13.2 26701 15.8
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 1.394 1.492 0.81 0.62 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 1.394 39.35 26071 1283 72.532 0.189 0.1872 0.1871 0.2271 0.2278 19.011
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] 0.005 0.044 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.393 r_dihedral_angle_3_deg 13.539 r_dihedral_angle_2_deg 11.806 r_lrange_it 8.258 r_lrange_other 8.035 r_dihedral_angle_1_deg 7.272 r_scangle_other 5.591 r_scangle_it 5.585 r_mcangle_it 3.796 r_mcangle_other 3.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.393 r_dihedral_angle_3_deg 13.539 r_dihedral_angle_2_deg 11.806 r_lrange_it 8.258 r_lrange_other 8.035 r_dihedral_angle_1_deg 7.272 r_scangle_other 5.591 r_scangle_it 5.585 r_mcangle_it 3.796 r_mcangle_other 3.794 r_scbond_other 3.446 r_scbond_it 3.444 r_mcbond_it 2.347 r_mcbond_other 2.347 r_angle_refined_deg 1.945 r_angle_other_deg 0.683 r_xyhbond_nbd_refined 0.226 r_symmetry_nbd_refined 0.22 r_nbd_refined 0.213 r_symmetry_xyhbond_nbd_refined 0.202 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.18 r_metal_ion_refined 0.168 r_nbd_other 0.164 r_chiral_restr 0.104 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1200 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 53
Software Software Software Name Purpose autoPROC data processing REFMAC refinement Coot model building autoPROC data reduction autoPROC data scaling REFMAC phasing