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Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) 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: 20.4 mg/mL
PCP-IP8: 10mM
Precipitant condition: 26% PEG 6K, 0.1M NaOAc pH 5, 0.2M LiCl, 10mM MgCl2
Ratio: 1:1
Crystal Properties Matthews coefficient Solvent content 2.6 53.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.861 α = 90 b = 65.512 β = 90 c = 77.482 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 2023-06-09 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 1.69 50.02 100 0.02 0.99 20.6 12.9 20308 26.9
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 1.69 1.726 0.34 0.86 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 1.697 50.02 20308 1011 99.946 0.172 0.1699 0.1841 0.21 0.2209 29.058
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] -0.647 -2.06 2.708
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.259 r_dihedral_angle_3_deg 14.637 r_dihedral_angle_2_deg 10.544 r_lrange_it 8.749 r_lrange_other 8.693 r_scangle_it 6.702 r_scangle_other 6.651 r_dihedral_angle_1_deg 6.314 r_scbond_it 4.222 r_scbond_other 4.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.259 r_dihedral_angle_3_deg 14.637 r_dihedral_angle_2_deg 10.544 r_lrange_it 8.749 r_lrange_other 8.693 r_scangle_it 6.702 r_scangle_other 6.651 r_dihedral_angle_1_deg 6.314 r_scbond_it 4.222 r_scbond_other 4.192 r_mcangle_it 3.677 r_mcangle_other 3.675 r_mcbond_it 2.639 r_mcbond_other 2.638 r_angle_refined_deg 1.756 r_angle_other_deg 0.603 r_metal_ion_refined 0.323 r_symmetry_nbd_refined 0.26 r_nbd_refined 0.211 r_nbd_other 0.206 r_symmetry_xyhbond_nbd_refined 0.202 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_other 0.189 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.177 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.082 r_xyhbond_nbd_other 0.02 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1202 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 62
Software Software Software Name Purpose autoPROC data processing REFMAC refinement Coot model building autoPROC data reduction autoPROC data scaling REFMAC phasing