2G45

Co-crystal structure of znf ubp domain from the deubiquitinating enzyme isopeptidase T (isot) in complex with ubiquitin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2G43PDB ENTRY 2G43

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.530016% polyethylene glycol 8000, 80 mM sodium cacodylate pH 6.5, 160 mM magenesium or calcium acetate, 20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 300K, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
3.2562.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.074α = 90
b = 68.074β = 90
c = 225.345γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-07-09MSINGLE WAVELENGTH
21x-rayMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0, 1.28317, 1.27163, 1.28855, 1.28237APS22-ID

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
2,11.993599.90.08713.910.440453-323.9
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)
1.992.061000.3677

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 ENTRY 2G431.99354045339760399098.50.2290.2290.268RANDOM41.8
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]
5.521.935.52-11.05
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.6
c_scangle_it2.89
c_mcangle_it2.02
c_scbond_it1.88
c_angle_deg1.3
c_mcbond_it1.26
c_improper_angle_d0.74
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.6
c_scangle_it2.89
c_mcangle_it2.02
c_scbond_it1.88
c_angle_deg1.3
c_mcbond_it1.26
c_improper_angle_d0.74
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3034
Nucleic Acid Atoms
Solvent Atoms203
Heterogen Atoms3

Software

Software
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction