X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IBIPDB ENTRIES 2IBI, 2G43, 2DAK, 2DAG
experimental modelPDB 2G43PDB ENTRIES 2IBI, 2G43, 2DAK, 2DAG
experimental modelPDB 2DAKPDB ENTRIES 2IBI, 2G43, 2DAK, 2DAG
experimental modelPDB 2DAGPDB ENTRIES 2IBI, 2G43, 2DAK, 2DAG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5298Crystals of the covalent ubiquitin complex of Usp5 were grown at 298 K using the hanging drop method by mixing equal volumes of protein solution (25 mg/ml) and Crystallization Buffer (1.45 M ammonium sulfate, 0.1 M bis-Tris, pH 6.5, 0.2 M sodium acetate, 5% ethyleneglycol and 1 mM dithiothreitol). The crystals were cryoprotected by immersion in Paratone N in paraffin oil 30% (v/v) and placed in liquid nitrogen., VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
3.2261.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.295α = 90
b = 188.845β = 90
c = 207.86γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMIRRORS2007-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-BAPS23-ID-B

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
12.835980.10117.15.466229-3
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)
2.82.994.60.84525.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 2IBI, 2G43, 2DAK, 2DAG2.834.962592329898.050.226880.224310.27588RANDOM73.948
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]
-0.350.39-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.014
r_dihedral_angle_4_deg19.923
r_dihedral_angle_3_deg19.655
r_dihedral_angle_1_deg5.975
r_scangle_it2.237
r_angle_refined_deg1.308
r_scbond_it1.275
r_mcangle_it0.898
r_mcbond_it0.469
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.014
r_dihedral_angle_4_deg19.923
r_dihedral_angle_3_deg19.655
r_dihedral_angle_1_deg5.975
r_scangle_it2.237
r_angle_refined_deg1.308
r_scbond_it1.275
r_mcangle_it0.898
r_mcbond_it0.469
r_chiral_restr0.09
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11759
Nucleic Acid Atoms
Solvent Atoms32
Heterogen Atoms9

Software

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