1VJV

Crystal structure of Ubiquitin carboxyl-terminal hydrolase 6 (yfr010w) from Saccharomyces cerevisiae at 1.74 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP27716% PEG MME 2000, 0.03M Tris_base, 0.07M Tris Cl , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2VAPOR DIFFUSION,SITTING DROP,NANODROP27721% PEG MME 2000, 0.03M Tris_base, 0.07M Tris Cl , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1442.44
2.2945.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.231α = 90
b = 79.449β = 90
c = 106.339γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC2003-07-25MSINGLE WAVELENGTH
21x-ray100CCDAPSwater cooled, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror2003-07-17MMAD
1,21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1
2SYNCHROTRONAPS BEAMLINE 19-BM0.96112, 0.97963,0.97946APS19-BM

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
1,21.7479.4598.20.05215.344282336.27
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)
1,21.741.7989.80.5942.12.82820

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.7463.6540625212999.020.180690.179170.20892RANDOM21.059
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]
-2.920.322.59
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it7.49
r_dihedral_angle_1_deg5.866
r_scbond_it5.018
r_mcangle_it3.126
r_mcbond_it1.889
r_angle_refined_deg1.304
r_angle_other_deg0.767
r_symmetry_vdw_other0.294
r_nbd_other0.238
r_nbd_refined0.201
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it7.49
r_dihedral_angle_1_deg5.866
r_scbond_it5.018
r_mcangle_it3.126
r_mcbond_it1.889
r_angle_refined_deg1.304
r_angle_other_deg0.767
r_symmetry_vdw_other0.294
r_nbd_other0.238
r_nbd_refined0.201
r_symmetry_vdw_refined0.186
r_symmetry_hbond_refined0.165
r_xyhbond_nbd_refined0.139
r_chiral_restr0.086
r_nbtor_other0.084
r_bond_refined_d0.016
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2964
Nucleic Acid Atoms
Solvent Atoms241
Heterogen Atoms

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
autoSHARPphasing
SOLOMONphasing
REFMACrefinement
CCP4data scaling