3DXB

Structure of the UHM domain of Puf60 fused to thioredoxin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72931.4M ammonium sulfate, 0.05M K-formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5551.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.12α = 90
b = 89.43β = 90
c = 299.39γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDLN2 cooled fixed-exit Si(111) monochromator Dynamically bendable mirror Beamline suitable for large unit cell structures2007-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.006SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.249.83299.80.110.10614.536.11031281029161136.481
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.3398.90.3930.6043.245.816266

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 REPLACEMENTTHROUGHOUT8 thioredoxin domains: PDB entry 2TRX 8 Puf60-UHM domains: homology model based on PDB 2pe82.249.752103128102916518199.80.214190.214190.21120.27148RANDOM21.623
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]
1.99-1.26-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.874
r_dihedral_angle_4_deg17.097
r_dihedral_angle_3_deg15.816
r_dihedral_angle_1_deg5.682
r_angle_refined_deg1.012
r_scangle_it0.921
r_scbond_it0.597
r_mcangle_it0.432
r_mcbond_it0.341
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.874
r_dihedral_angle_4_deg17.097
r_dihedral_angle_3_deg15.816
r_dihedral_angle_1_deg5.682
r_angle_refined_deg1.012
r_scangle_it0.921
r_scbond_it0.597
r_mcangle_it0.432
r_mcbond_it0.341
r_nbtor_refined0.298
r_nbd_refined0.191
r_symmetry_vdw_refined0.148
r_xyhbond_nbd_refined0.13
r_symmetry_hbond_refined0.107
r_chiral_restr0.066
r_bond_refined_d0.006
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13074
Nucleic Acid Atoms
Solvent Atoms1191
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
XDSdata reduction
XDSdata scaling
PHASERphasing