5XU8

Crystal structure of human USP2 in complex with ubiquitin and 6-thioguanine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HD5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729524.5% PEG3350, 0.2 M MgC12, 0.1 M Bis-Tris
Crystal Properties
Matthews coefficientSolvent content
1.9637.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.953α = 90
b = 54.65β = 107.54
c = 72.687γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2013-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A10.976NSRRCBL15A1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.83097.919.93.733397
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8680.13.5

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 REPLACEMENTTHROUGHOUT2hd51.813033397172599.520.181510.178540.23827RANDOM39.95
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]
-30.75-0.882.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.19
r_dihedral_angle_4_deg18.815
r_dihedral_angle_3_deg14.842
r_long_range_B_refined9.093
r_dihedral_angle_1_deg6.233
r_mcangle_it3.921
r_scbond_it3.68
r_mcbond_it2.7
r_angle_refined_deg1.487
r_chiral_restr0.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.19
r_dihedral_angle_4_deg18.815
r_dihedral_angle_3_deg14.842
r_long_range_B_refined9.093
r_dihedral_angle_1_deg6.233
r_mcangle_it3.921
r_scbond_it3.68
r_mcbond_it2.7
r_angle_refined_deg1.487
r_chiral_restr0.103
r_bond_refined_d0.012
r_gen_planes_refined0.007
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
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 Atoms3255
Nucleic Acid Atoms
Solvent Atoms261
Heterogen Atoms22

Software

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