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Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) R89S 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 conditions: 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 = 34.288 α = 90 b = 65.483 β = 90 c = 78.949 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 9M 2023-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
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 1.4 39.47 94.1 0.04 0.99 11.1 12.6 28543 13.9
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 1.4 1.51 0.483 0.673 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 1.408 39.47 28541 1379 80.997 0.172 0.1695 0.1695 0.2113 0.2113 16.493
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] -0.132 0.109 0.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.997 r_dihedral_angle_3_deg 13.349 r_dihedral_angle_2_deg 8.851 r_lrange_it 7.259 r_lrange_other 6.972 r_dihedral_angle_1_deg 6.479 r_scangle_it 4.853 r_scangle_other 4.851 r_scbond_it 3.119 r_scbond_other 3.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.997 r_dihedral_angle_3_deg 13.349 r_dihedral_angle_2_deg 8.851 r_lrange_it 7.259 r_lrange_other 6.972 r_dihedral_angle_1_deg 6.479 r_scangle_it 4.853 r_scangle_other 4.851 r_scbond_it 3.119 r_scbond_other 3.118 r_mcangle_it 2.976 r_mcangle_other 2.974 r_angle_refined_deg 1.9 r_mcbond_other 1.897 r_mcbond_it 1.896 r_angle_other_deg 0.651 r_symmetry_nbd_refined 0.274 r_symmetry_xyhbond_nbd_refined 0.242 r_nbd_other 0.238 r_xyhbond_nbd_refined 0.216 r_nbd_refined 0.205 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.175 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.083 r_xyhbond_nbd_other 0.037 r_symmetry_xyhbond_nbd_other 0.019 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_metal_ion_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1174 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 47
Software Software Software Name Purpose autoPROC data processing REFMAC refinement Coot model building autoPROC data reduction autoPROC data scaling REFMAC phasing