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Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) R41A mutant in complex with IP6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 Protein: 20mg/mL
IP6: 10mM
Precipitant conditions: 30% PEG 6K, 0.1M NaOAc pH 5, 0.2M LiCl, 1mM MgCl2
Ratio: 2:1
Crystal Properties Matthews coefficient Solvent content 2.6 53.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.592 α = 90 b = 65.496 β = 90 c = 77.695 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 EIGER X 9M 2023-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
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 1.24 50.08 88 0.02 0.99 12.78 11.4 33878 16
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 1.24 1.37 0.43 0.78 1.57
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 1.24 50.077 33878 1768 66.498 0.171 0.169 0.1688 0.206 0.2058 17.5
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] -0.142 -0.036 0.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.007 r_dihedral_angle_3_deg 12.429 r_dihedral_angle_2_deg 10.029 r_lrange_it 7.915 r_lrange_other 7.743 r_dihedral_angle_1_deg 6.515 r_scangle_it 5.481 r_scangle_other 5.481 r_scbond_it 3.441 r_scbond_other 3.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.007 r_dihedral_angle_3_deg 12.429 r_dihedral_angle_2_deg 10.029 r_lrange_it 7.915 r_lrange_other 7.743 r_dihedral_angle_1_deg 6.515 r_scangle_it 5.481 r_scangle_other 5.481 r_scbond_it 3.441 r_scbond_other 3.439 r_mcangle_it 3.042 r_mcangle_other 3.04 r_angle_refined_deg 2.033 r_mcbond_it 2.029 r_mcbond_other 2.028 r_angle_other_deg 0.677 r_nbd_other 0.224 r_symmetry_xyhbond_nbd_refined 0.223 r_nbd_refined 0.207 r_symmetry_nbd_refined 0.191 r_symmetry_nbd_other 0.189 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.174 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1196 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 48
Software Software Software Name Purpose autoPROC data processing REFMAC refinement Coot model building autoPROC data reduction autoPROC data scaling REFMAC phasing