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Crystal Structure of Parkin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K7D PDB entries: 4K7D (rat parkin 141-465) and 2ZEQ (mouse parkin 1-72) experimental model PDB 2ZEQ PDB entries: 4K7D (rat parkin 141-465) and 2ZEQ (mouse parkin 1-72)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 22.5% PEG3350, 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.0, 10% (v/v) glycerol, 3% sorbitol and 25 mM 2-mercaptoethanol, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.91 57.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.598 α = 90 b = 277.439 β = 90 c = 125.891 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 210 mirrors 2012-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F2 0.9183 CHESS F2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 6.5 50 99.8 0.172 15.1 7.2 14952 14922 1 1 227
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 6.5 6.73 100 0.805 2.5 7.3 1463
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB entries: 4K7D (rat parkin 141-465) and 2ZEQ (mouse parkin 1-72) 6.499 49.334 1.34 14952 14865 749 99.4 0.3078 0.3068 0.3042 0.3266 0.3288 random 88.6785
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 14.795 f_angle_d 1.174 f_chiral_restr 0.079 f_bond_d 0.011 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 35328 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 96
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing