2BWB

Crystal structure of the UBA domain of Dsk2 from S. cerevisiae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.51.6 M TRISODIUM CITRATE PH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.448.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.311α = 90
b = 44.069β = 114.87
c = 111.525γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2003-05-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.329.599.90.0916.44231346
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)
12.32.421000.283.83.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.3101.0222007112799.80.2460.2430.307RANDOM72.39
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
r_dihedral_angle_2_deg39.928
r_dihedral_angle_3_deg19.544
r_dihedral_angle_4_deg17.23
r_dihedral_angle_1_deg8.997
r_scangle_it1.151
r_angle_refined_deg1.15
r_angle_other_deg0.828
r_scbond_it0.741
r_mcangle_it0.422
r_mcbond_it0.357
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.928
r_dihedral_angle_3_deg19.544
r_dihedral_angle_4_deg17.23
r_dihedral_angle_1_deg8.997
r_scangle_it1.151
r_angle_refined_deg1.15
r_angle_other_deg0.828
r_scbond_it0.741
r_mcangle_it0.422
r_mcbond_it0.357
r_symmetry_vdw_other0.243
r_symmetry_vdw_refined0.229
r_symmetry_hbond_refined0.205
r_nbd_refined0.2
r_xyhbond_nbd_refined0.193
r_nbd_other0.173
r_nbtor_refined0.17
r_nbtor_other0.087
r_chiral_restr0.062
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3187
Nucleic Acid Atoms
Solvent Atoms150
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing