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Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) in complex with IP6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 Protein: 20 mg/mL
IP6: 10 mM
Precipitant condition: 28% PEG 6K, 0.1M NaOAc pH 5, 0.2M LiCl and 1mM MgCl2
Ratio: 1:1
Crystal Properties Matthews coefficient Solvent content 2.6 53.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.574 α = 90 b = 65.682 β = 90 c = 79.13 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 2023-05-05 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 1.28 50.54 91.5 0.02 0.99 14.7 12.7 38659 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 1.28 1.37 0.3 0.8 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 1.28 50.54 38659 1938 80.978 0.17 0.1687 0.1683 0.1923 0.1919 16.934
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] -0.084 -0.07 0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.775 r_dihedral_angle_3_deg 12.873 r_dihedral_angle_2_deg 11.745 r_lrange_it 7.793 r_lrange_other 7.509 r_dihedral_angle_1_deg 6.59 r_scangle_other 5.648 r_scangle_it 5.631 r_scbond_it 3.522 r_scbond_other 3.501
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.775 r_dihedral_angle_3_deg 12.873 r_dihedral_angle_2_deg 11.745 r_lrange_it 7.793 r_lrange_other 7.509 r_dihedral_angle_1_deg 6.59 r_scangle_other 5.648 r_scangle_it 5.631 r_scbond_it 3.522 r_scbond_other 3.501 r_mcangle_it 3.14 r_mcangle_other 3.138 r_angle_refined_deg 1.997 r_mcbond_it 1.996 r_mcbond_other 1.995 r_angle_other_deg 0.665 r_symmetry_nbd_refined 0.273 r_metal_ion_refined 0.241 r_nbd_other 0.229 r_nbd_refined 0.213 r_symmetry_xyhbond_nbd_refined 0.212 r_xyhbond_nbd_refined 0.199 r_symmetry_nbd_other 0.196 r_symmetry_xyhbond_nbd_other 0.179 r_nbtor_refined 0.171 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1202 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 47
Software Software Software Name Purpose autoPROC data processing REFMAC refinement Coot model building REFMAC phasing autoPROC data reduction autoPROC data scaling