X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4K7DPDB entries: 4K7D (rat parkin 141-465) and 2ZEQ (mouse parkin 1-72)
experimental modelPDB 2ZEQPDB entries: 4K7D (rat parkin 141-465) and 2ZEQ (mouse parkin 1-72)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727722.5% 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 coefficientSolvent content
2.9157.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 208.598α = 90
b = 277.439β = 90
c = 125.891γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210mirrors2012-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F20.9183CHESSF2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
16.55099.80.17215.17.2149521492211227
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
16.56.731000.8052.57.31463

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB entries: 4K7D (rat parkin 141-465) and 2ZEQ (mouse parkin 1-72)6.49949.3341.34149521486574999.40.30780.30680.3266random88.6785
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.795
f_angle_d1.174
f_chiral_restr0.079
f_bond_d0.011
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms35328
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms96

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing