☰ Navigation Tabs
Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) R89S mutant in complex with 1,5-(PCP)-IP5 (PCP-IP8)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 Protein: 21.5mg/mL
PCP-IP8: 10mM
Precipitant condition: 26% PEG 6K, 0.1M NaOAc pH 5, 0.2M LiCl, 1mM MgCl2
Ratio: 1:1
Crystal Properties Matthews coefficient Solvent content 2.6 52.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.514 α = 90 b = 65.232 β = 90 c = 78.543 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 EIGER2 X 9M 2023-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313 ESRF ID30B
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 1.63 78.54 93.7 0.03 0.998 13 11.8 21427 26.6
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 1.63 1.66 0.727 0.519 1.2
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.63 50.182 21377 1063 93.595 0.185 0.1831 0.1961 0.2183 0.2343 RANDOM 31.68
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] -0.994 -1.399 2.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.007 r_dihedral_angle_3_deg 12.455 r_lrange_it 11.592 r_lrange_other 11.59 r_scangle_it 9.281 r_scangle_other 9.277 r_dihedral_angle_2_deg 9.268 r_dihedral_angle_1_deg 6.378 r_scbond_it 6.05 r_scbond_other 6.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.007 r_dihedral_angle_3_deg 12.455 r_lrange_it 11.592 r_lrange_other 11.59 r_scangle_it 9.281 r_scangle_other 9.277 r_dihedral_angle_2_deg 9.268 r_dihedral_angle_1_deg 6.378 r_scbond_it 6.05 r_scbond_other 6.047 r_mcangle_it 3.699 r_mcangle_other 3.698 r_mcbond_it 2.714 r_mcbond_other 2.713 r_angle_refined_deg 1.919 r_angle_other_deg 0.641 r_symmetry_nbd_refined 0.264 r_symmetry_xyhbond_nbd_refined 0.24 r_nbd_other 0.233 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.197 r_symmetry_nbd_other 0.19 r_symmetry_xyhbond_nbd_other 0.179 r_nbtor_refined 0.178 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.085 r_metal_ion_refined 0.054 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1141 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 53
Software Software Software Name Purpose autoPROC data processing Aimless data scaling REFMAC refinement Coot model building REFMAC phasing autoPROC data reduction