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Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) R89S mutant in complex with 1,5-(PCP)-IP5 (PCP-IP8)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WOG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 Protein: 20mg/mL
PCP-IP8: 10mM
Precipitant condition: 20% PEG 6K, 0.1M NaOAc pH 5, 0.2M LiCl,10mM MgCl2
Ratio: 1:1
Crystal Properties Matthews coefficient Solvent content 2.6 53.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.272 α = 90 b = 65.07 β = 90 c = 78.416 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 PILATUS 6M 2022-05-05 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 78.42 100 0.03 0.999 13.8 12.2 28885 19.6
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 1.5 1.53 0.661 0.521 1.3
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 MOLECULAR REPLACEMENT THROUGHOUT 1.5 50.075 28825 1444 99.965 0.177 0.1758 0.181 0.1954 0.1997 RANDOM 23.516
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] -1.628 -1.089 2.717
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.476 r_dihedral_angle_3_deg 13.363 r_dihedral_angle_2_deg 9.586 r_lrange_it 7.657 r_lrange_other 7.459 r_dihedral_angle_1_deg 6.857 r_scangle_it 6.13 r_scangle_other 6.127 r_scbond_other 3.745 r_scbond_it 3.736
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.476 r_dihedral_angle_3_deg 13.363 r_dihedral_angle_2_deg 9.586 r_lrange_it 7.657 r_lrange_other 7.459 r_dihedral_angle_1_deg 6.857 r_scangle_it 6.13 r_scangle_other 6.127 r_scbond_other 3.745 r_scbond_it 3.736 r_mcangle_it 3.033 r_mcangle_other 3.031 r_mcbond_it 2.112 r_mcbond_other 2.111 r_angle_refined_deg 1.912 r_angle_other_deg 0.651 r_symmetry_nbd_refined 0.338 r_metal_ion_refined 0.248 r_xyhbond_nbd_refined 0.237 r_nbd_refined 0.215 r_nbd_other 0.194 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.135 r_symmetry_xyhbond_nbd_other 0.113 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.009 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 1141 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 49
Software Software Software Name Purpose autoPROC data reduction Aimless data scaling MOLREP phasing REFMAC refinement Coot model building