1VJV
Crystal structure of Ubiquitin carboxyl-terminal hydrolase 6 (yfr010w) from Saccharomyces cerevisiae at 1.74 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 277 | 16% PEG MME 2000, 0.03M Tris_base, 0.07M Tris Cl , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K | |
2 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 277 | 21% PEG MME 2000, 0.03M Tris_base, 0.07M Tris Cl , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.44 |
2.29 | 45.77 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.231 | α = 90 |
b = 79.449 | β = 90 |
c = 106.339 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC | 2003-07-25 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | APS | water cooled, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror | 2003-07-17 | M | MAD | |||||
1,2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | ALS | 8.3.1 | |
2 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.96112, 0.97963,0.97946 | APS | 19-BM |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1,2 | 1.74 | 79.45 | 98.2 | 0.052 | 15.3 | 4 | 42823 | 36.27 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1,2 | 1.74 | 1.79 | 89.8 | 0.594 | 2.1 | 2.8 | 2820 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 1.74 | 63.65 | 40625 | 2129 | 99.02 | 0.18069 | 0.17917 | 0.20892 | RANDOM | 21.059 |
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] | |
-2.92 | 0.32 | 2.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_it | 7.49 |
r_dihedral_angle_1_deg | 5.866 |
r_scbond_it | 5.018 |
r_mcangle_it | 3.126 |
r_mcbond_it | 1.889 |
r_angle_refined_deg | 1.304 |
r_angle_other_deg | 0.767 |
r_symmetry_vdw_other | 0.294 |
r_nbd_other | 0.238 |
r_nbd_refined | 0.201 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2964 |
Nucleic Acid Atoms | |
Solvent Atoms | 241 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
SHELXD | phasing |
autoSHARP | phasing |
SOLOMON | phasing |
REFMAC | refinement |
CCP4 | data scaling |