5XVE

Crystal structure of human USP2 C276S mutant in complex with ubiquitin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829521% PEG3350, 8% Tacsimate (pH8.0)
Crystal Properties
Matthews coefficientSolvent content
1.9837.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.473α = 90
b = 54.011β = 107.79
c = 74.753γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13C10.976NSRRCBL13C1

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
11.243098.50.034333.6102971
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)
11.241.2896.90.2413.4

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 REPLACEMENTTHROUGHOUT2HD51.2430102800558798.440.147840.146940.16403RANDOM15.025
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]
-0.640.180.310.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.229
r_sphericity_free20.77
r_dihedral_angle_4_deg16.265
r_dihedral_angle_3_deg11.958
r_dihedral_angle_1_deg6.019
r_sphericity_bonded5.003
r_long_range_B_refined2.003
r_long_range_B_other1.665
r_angle_refined_deg1.246
r_rigid_bond_restr1.173
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.229
r_sphericity_free20.77
r_dihedral_angle_4_deg16.265
r_dihedral_angle_3_deg11.958
r_dihedral_angle_1_deg6.019
r_sphericity_bonded5.003
r_long_range_B_refined2.003
r_long_range_B_other1.665
r_angle_refined_deg1.246
r_rigid_bond_restr1.173
r_scangle_other1.135
r_mcangle_it1.013
r_mcangle_other1.013
r_scbond_it0.927
r_scbond_other0.927
r_angle_other_deg0.877
r_mcbond_it0.77
r_mcbond_other0.769
r_chiral_restr0.075
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3284
Nucleic Acid Atoms
Solvent Atoms356
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data processing
PHASERmodel building
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling