4E08

Crystal structure of Drosophila melanogaster DJ-1beta


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.629825% polyethylene glycol 4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate pH=4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3146.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.52α = 90
b = 52.52β = 90
c = 227.173γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARMOSAIC 300 mm CCDK-B PAIR OF BIOMORPH MIRRORS2010-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.98APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
127697.30.09821.18.5251162511626.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0783.90.5871.85.12112

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2OR3275.722381423814126797.480.195790.195790.193180.24559RANDOM31.734
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]
1.790.91.79-2.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.144
r_dihedral_angle_4_deg22.047
r_dihedral_angle_3_deg14.536
r_dihedral_angle_1_deg6.069
r_angle_refined_deg1.503
r_chiral_restr0.096
r_bond_refined_d0.016
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2680
Nucleic Acid Atoms
Solvent Atoms278
Heterogen Atoms5

Software

Software
Software NamePurpose
JBluIce-EPICSdata collection
PHASERphasing
PHENIXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing