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Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) N112S mutant in complex with IP6
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: 24mg/mL
Ip6: 10mM
Precipitant condition: 31% PEG 6K, 0.1M NaOAc pH 5, 0.2M LiCl, 10mM MgCl2.
Ratio: 1:1
Crystal Properties Matthews coefficient Solvent content 2.9 58.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.131 α = 90 b = 100.131 β = 90 c = 34.06 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 EIGER X 4M 2023-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.96770 ESRF MASSIF-3
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 1.78 50.07 100 0.13 0.99 4.5 15.9 19071 18.6
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 1.78 1.81 6.95 0.33 0.1
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 1.78 50.07 19071 861 99.953 0.189 0.1867 0.1954 0.2421 0.2439 22.887
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] 0.183 0.092 0.183 -0.594
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.511 r_dihedral_angle_3_deg 12.789 r_dihedral_angle_2_deg 9.957 r_lrange_it 8.312 r_lrange_other 8.21 r_dihedral_angle_1_deg 6.867 r_scangle_it 5.196 r_scangle_other 5.191 r_mcangle_it 3.38 r_mcangle_other 3.379
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.511 r_dihedral_angle_3_deg 12.789 r_dihedral_angle_2_deg 9.957 r_lrange_it 8.312 r_lrange_other 8.21 r_dihedral_angle_1_deg 6.867 r_scangle_it 5.196 r_scangle_other 5.191 r_mcangle_it 3.38 r_mcangle_other 3.379 r_scbond_it 3.252 r_scbond_other 3.133 r_mcbond_it 2.071 r_mcbond_other 2.071 r_angle_refined_deg 1.667 r_angle_other_deg 0.558 r_symmetry_nbd_refined 0.257 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.192 r_symmetry_nbd_other 0.191 r_symmetry_xyhbond_nbd_refined 0.189 r_nbd_other 0.181 r_nbtor_refined 0.174 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.075 r_metal_ion_refined 0.051 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1200 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 48
Software Software Software Name Purpose autoPROC data processing MOLREP phasing REFMAC refinement Coot model building autoPROC data reduction autoPROC data scaling REFMAC phasing