3JYU

Crystal structure of the N-terminal domains of the ubiquitin specific peptidase 4 (USP4)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W6Vpdb entry 1W6V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.22911 volume of 9 mg/ml protein solution was mixed with 1 volume of a solution of 20% (w/v) PEG 4000, 10% (v/v) isopropanool, 0.1 M sodium HEPES, and 0.001 M dithiothreitol and equilibrated against 1 M NaCl (well solution). The crystal was cryoprotected in well solution mixed 1:1 with a solution containing 60% (v/v) ethylene glycol and 200 mg/ml 3-(1-pyridino)-propene sulfonate (NDSB-201) and frozen by immersion in liquid nitrogen, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.5852.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 180.06α = 90
b = 34.06β = 133.52
c = 125.19γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210Si(111) double-crystal monochromator2006-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID0.97942APS17-ID

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
12.3745.499.10.0960.10411.96.92282022745339.28
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)
2.372.598.40.3490.384.16.53246

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMRSADpdb entry 1W6V2.3741.2271.3722421111097.390.18440.18190.2334RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.658
f_angle_d1.062
f_chiral_restr0.07
f_bond_d0.008
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3523
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms13

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXmodel building
SHARPphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing