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Crystal Structure of Parkin E3 ubiquitin ligase (linker deletion; delta 86-130)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K7D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 0.3M Ammonium Sulfate, 0.1M HEPES pH 7.5, 18% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.47 50.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.105 α = 90 b = 114.105 β = 90 c = 186.399 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 CCD RIGAKU SATURN 944+ 2012-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.54 50 95 0.128 0.131 0.047 6.2 8.1 28338
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 2.54 2.58 69 0.123 2.7 1040
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4K7D 2.54 36.62 28036 1485 98.95 0.1947 0.1925 0.1638 0.2353 0.1936 RANDOM 66.684
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] 1.9 1.9 -3.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.781 r_dihedral_angle_3_deg 17.471 r_dihedral_angle_4_deg 16.416 r_dihedral_angle_1_deg 5.77 r_mcangle_it 3.334 r_mcbond_it 1.96 r_mcbond_other 1.96 r_angle_refined_deg 1.332 r_angle_other_deg 0.968 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.781 r_dihedral_angle_3_deg 17.471 r_dihedral_angle_4_deg 16.416 r_dihedral_angle_1_deg 5.77 r_mcangle_it 3.334 r_mcbond_it 1.96 r_mcbond_other 1.96 r_angle_refined_deg 1.332 r_angle_other_deg 0.968 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5673 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement StructureStudio data collection PDB_EXTRACT data extraction XDS data scaling MOLREP phasing XDS data reduction