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Crystal structure of parkin (R0RB):2pUb with activator compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7US1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 0.2 M Sodium Chloride, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.99 58.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.54 α = 90 b = 83.54 β = 90 c = 258.77 γ = 120
Symmetry Space Group P 61 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 EIGER X 9M 2023-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.953 CLSI 08ID-1
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 2.5 48.22 99.95 0.11 0.112 0.018 1 24.08 38.3 19414 76.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 100 2.938 2.98 0.464 0.718 1.72 40.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.5 48.22 1.34 19414 971 99.98 0.2423 0.2397 0.2396 0.2937 0.2943 89.24
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.1638 f_angle_d 1.2809 f_chiral_restr 0.0699 f_bond_d 0.0103 f_plane_restr 0.0097
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2970 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction PHENIX phasing Coot model building