☰ Navigation Tabs
Crystal Structure of isolated Death Domain of human p53-induced protein PIDD (778-873) with Thr788Asp phosphomimetic mutation.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OF5 Chain H was used.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 290 100 mM Tris pH 8, 25%
v/v polyethylene glycol (PEG) 350 MME
Crystal Properties Matthews coefficient Solvent content 2 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.97 α = 90 b = 60.97 β = 90 c = 65.916 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 EIGER2 XE 16M 2023-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976223 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.8 52.81 100 0.14 0.148 0.045 0.998 9.6 9 25417 25.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 99.8 0.599 8.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 52.8 25393 1182 99.98 0.183 0.1818 0.1817 0.2115 0.211 RANDOM 30.119
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] 0.302 0.151 0.302 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.712 r_dihedral_angle_3_deg 12.135 r_dihedral_angle_2_deg 8.186 r_dihedral_angle_1_deg 5.823 r_lrange_it 5.648 r_lrange_other 5.621 r_scangle_it 4.129 r_scangle_other 4.128 r_scbond_it 2.586 r_scbond_other 2.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.712 r_dihedral_angle_3_deg 12.135 r_dihedral_angle_2_deg 8.186 r_dihedral_angle_1_deg 5.823 r_lrange_it 5.648 r_lrange_other 5.621 r_scangle_it 4.129 r_scangle_other 4.128 r_scbond_it 2.586 r_scbond_other 2.585 r_mcangle_it 2.205 r_mcangle_other 2.204 r_mcbond_it 1.508 r_mcbond_other 1.508 r_angle_refined_deg 0.926 r_angle_other_deg 0.395 r_nbd_refined 0.219 r_nbd_other 0.175 r_symmetry_nbd_other 0.17 r_nbtor_refined 0.161 r_symmetry_nbd_refined 0.14 r_symmetry_xyhbond_nbd_refined 0.139 r_xyhbond_nbd_refined 0.118 r_ncsr_local_group_2 0.093 r_ncsr_local_group_1 0.086 r_ncsr_local_group_3 0.086 r_symmetry_nbtor_other 0.061 r_chiral_restr 0.053 r_bond_refined_d 0.012 r_bond_other_d 0.004 r_gen_planes_refined 0.002 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2300 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement REFMAC refinement DIALS data reduction Coot model building xia2 data reduction MOLREP phasing Aimless data scaling