3IFW

Crystal structure of the S18Y variant of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP92982.4 M ammonium sulfate, 0.1M BICINE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.141.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.304α = 90
b = 87.304β = 90
c = 193.544γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrors2009-02-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0032APS23-ID-D

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
12.45098.50.0940.094219.9112481124822
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)
2.42.4499.80.60.636.4

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 2ETL PDB ENTRY 1XD3, CHAIN B2.450112481069953998.170.211050.20890.25627RANDOM79.609
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]
0.040.020.04-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.933
r_dihedral_angle_3_deg15.346
r_dihedral_angle_4_deg12.056
r_dihedral_angle_1_deg4.923
r_angle_refined_deg0.896
r_scangle_it0.762
r_scbond_it0.507
r_nbtor_refined0.291
r_mcangle_it0.282
r_symmetry_vdw_refined0.186
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.933
r_dihedral_angle_3_deg15.346
r_dihedral_angle_4_deg12.056
r_dihedral_angle_1_deg4.923
r_angle_refined_deg0.896
r_scangle_it0.762
r_scbond_it0.507
r_nbtor_refined0.291
r_mcangle_it0.282
r_symmetry_vdw_refined0.186
r_nbd_refined0.172
r_mcbond_it0.162
r_xyhbond_nbd_refined0.097
r_symmetry_hbond_refined0.087
r_chiral_restr0.054
r_bond_refined_d0.007
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2344
Nucleic Acid Atoms
Solvent Atoms51
Heterogen Atoms8

Software

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