4DM9

The Crystal Structure of Ubiquitin Carboxy-terminal hydrolase L1 (UCHL1) bound to a tripeptide fluoromethyl ketone Z-VAE(OMe)-FMK


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72982.4M ammonium sulfate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.3146.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.011α = 90
b = 110.011β = 90
c = 78.745γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrors2006-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0APS23-ID-D

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
12.355098.10.05148.512.920719203262.12.1
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)
12.352.4389.60.4992.17.8

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT2ETL2.3534.8731.342070320267103797.890.19950.1970.2502
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]
8.9158.915-17.8301
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.536
f_angle_d1.048
f_chiral_restr0.088
f_bond_d0.005
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3547
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling