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Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) R41A mutant in complex with 5-(PP)-IP5 (5-IP7)
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: 20mg/mL
Precipitant condition: 29% PEG 6K, 0.1M NaOAc pH 5, 0.2M LiCl, 10mM MgCl2, 20mM NaF
Ratio: 1:1
Crystal Properties Matthews coefficient Solvent content 2.9 58.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.95 α = 90 b = 99.95 β = 90 c = 34.469 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 2024-04-13 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 86.56 99.8 0.05 0.99 9.7 16.7 31754 22.9
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 1.5 1.53 1.55 0.25 0.4
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.5 86.559 31464 1506 98.856 0.164 0.1625 0.1624 0.1848 0.185 24.684
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] -0.061 -0.031 -0.061 0.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.484 r_dihedral_angle_3_deg 13.793 r_lrange_it 9.803 r_lrange_other 9.018 r_dihedral_angle_2_deg 8.385 r_scangle_it 7.114 r_dihedral_angle_1_deg 6.741 r_scangle_other 6.645 r_scbond_it 4.628 r_scbond_other 4.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.484 r_dihedral_angle_3_deg 13.793 r_lrange_it 9.803 r_lrange_other 9.018 r_dihedral_angle_2_deg 8.385 r_scangle_it 7.114 r_dihedral_angle_1_deg 6.741 r_scangle_other 6.645 r_scbond_it 4.628 r_scbond_other 4.237 r_mcangle_it 3.901 r_mcangle_other 3.899 r_mcbond_it 2.657 r_mcbond_other 2.657 r_angle_refined_deg 1.963 r_angle_other_deg 0.716 r_symmetry_nbd_refined 0.271 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.202 r_symmetry_xyhbond_nbd_refined 0.199 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.176 r_nbd_other 0.175 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.086 r_metal_ion_refined 0.039 r_symmetry_xyhbond_nbd_other 0.017 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1196 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 61
Software Software Software Name Purpose xia2 data reduction xia2 data scaling MOLREP phasing REFMAC refinement Coot model building