2OOA

crystal structure of the UBA domain from Cbl-b ubiquitin ligase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.22931.2M sodium/potassium phosphate, 12% glycerol, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9938.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.138α = 90
b = 50.199β = 90
c = 78.343γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 4mirrors2005-08-28MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X8CNSLSX8C

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
11.565097.50.07129.25.9133321300311
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)
11.561.6289.50.2157.44.7883

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.5617.29133321237263197.530.2060.2060.20430.23992RANDOM16.835
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]
-0.040.010.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.99
r_dihedral_angle_4_deg24.025
r_dihedral_angle_3_deg11.777
r_dihedral_angle_1_deg4.993
r_scangle_it3.074
r_scbond_it1.846
r_angle_refined_deg1.26
r_mcangle_it0.964
r_mcbond_it0.654
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.99
r_dihedral_angle_4_deg24.025
r_dihedral_angle_3_deg11.777
r_dihedral_angle_1_deg4.993
r_scangle_it3.074
r_scbond_it1.846
r_angle_refined_deg1.26
r_mcangle_it0.964
r_mcbond_it0.654
r_nbtor_refined0.313
r_nbd_refined0.214
r_symmetry_hbond_refined0.2
r_symmetry_vdw_refined0.133
r_xyhbond_nbd_refined0.089
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms666
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing