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Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) E108N mutant
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 9 289 Protein: 20 mg/mL
Precipitant condition: 25% w/v PEG 1500, 0.1M SPG pH 9
Ratio: 1:1
Crystal Properties Matthews coefficient Solvent content 2.4 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.259 α = 90 b = 59.259 β = 90 c = 153.23 γ = 120
Symmetry Space Group P 65 2 2
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 2024-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97918 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 1.321 51.348 98.8 0.01 1 34.3 37.1 37944 23.3
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 1.321 1.344 0.3 0.87 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 1.426 51.32 30389 1551 99.22 0.188 0.1864 0.1955 0.2185 0.2336 26.567
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] 0.266 0.133 0.266 -0.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.204 r_dihedral_angle_3_deg 13.623 r_dihedral_angle_2_deg 11.212 r_lrange_other 8.2 r_lrange_it 8.194 r_dihedral_angle_1_deg 6.595 r_scangle_other 6.42 r_scangle_it 6.406 r_scbond_it 4.181 r_scbond_other 4.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.204 r_dihedral_angle_3_deg 13.623 r_dihedral_angle_2_deg 11.212 r_lrange_other 8.2 r_lrange_it 8.194 r_dihedral_angle_1_deg 6.595 r_scangle_other 6.42 r_scangle_it 6.406 r_scbond_it 4.181 r_scbond_other 4.18 r_mcangle_it 3.941 r_mcangle_other 3.939 r_mcbond_it 2.821 r_mcbond_other 2.821 r_angle_refined_deg 2.146 r_angle_other_deg 0.736 r_symmetry_xyhbond_nbd_refined 0.206 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.195 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.179 r_symmetry_nbd_refined 0.176 r_nbd_other 0.168 r_chiral_restr 0.108 r_symmetry_nbtor_other 0.088 r_symmetry_xyhbond_nbd_other 0.05 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1161 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 11
Software Software Software Name Purpose autoPROC data processing MOLREP phasing REFMAC refinement Coot model building autoPROC data reduction autoPROC data scaling