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Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) in complex with 1,5-(PCP)-IP5 (PCP-IP8)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9T48
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 Protein: 20.4
PCP-IP8: 5mM
Precipitant condition: 27% PEG 6K, 0.1M NaOAc pH 5, 0.2M LiCl, 10mM MgCl2
Ratio: 1:1
Crystal Properties Matthews coefficient Solvent content 2.9 57.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.149 α = 90 b = 99.149 β = 90 c = 34.154 γ = 120
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 1.5 49.57 96.7 0.04 0.99 15.3 20.8 29778 15
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 1.5 1.53 0.4 0.8 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 MOLECULAR REPLACEMENT FREE R-VALUE 1.5 49.57 29778 1560 96.704 0.154 0.1531 0.1536 0.1792 0.1787 17.614
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] 0.253 0.127 0.253 -0.822
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.85 r_dihedral_angle_3_deg 12.059 r_lrange_it 9.044 r_lrange_other 8.808 r_dihedral_angle_1_deg 6.659 r_scangle_it 6.631 r_scangle_other 6.628 r_dihedral_angle_2_deg 6.283 r_scbond_other 4.172 r_scbond_it 4.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.85 r_dihedral_angle_3_deg 12.059 r_lrange_it 9.044 r_lrange_other 8.808 r_dihedral_angle_1_deg 6.659 r_scangle_it 6.631 r_scangle_other 6.628 r_dihedral_angle_2_deg 6.283 r_scbond_other 4.172 r_scbond_it 4.169 r_mcangle_it 3.27 r_mcangle_other 3.267 r_mcbond_other 2.152 r_mcbond_it 2.15 r_angle_refined_deg 2.144 r_angle_other_deg 0.707 r_symmetry_nbd_refined 0.269 r_symmetry_xyhbond_nbd_refined 0.253 r_nbd_other 0.246 r_xyhbond_nbd_refined 0.224 r_nbd_refined 0.218 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.181 r_metal_ion_refined 0.142 r_chiral_restr 0.109 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.014 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 1171 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 50
Software Software Software Name Purpose autoPROC data processing MOLREP phasing REFMAC refinement Coot model building autoPROC data reduction autoPROC data scaling