3V6C
Crystal Structure of USP2 in complex with mutated ubiquitin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2HD5 | pdb entry 2HD5 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 21% PEG 3350,0.2 M CaCl, 0.1 Bis-Tris pH 7.0, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.01 | 38.77 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.735 | α = 90 |
b = 84.077 | β = 90 |
c = 86.915 | 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 | RIGAKU SATURN A200 | 2011-11-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.54178 |
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 | 1.7 | 84.08 | 97.4 | 0.0579 | 19.49 | 6.39 | 46959 | 45718 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.7 | 1.75 | 72.3 | 2.31 | 2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 2HD5 | 1.7 | 84.08 | 46855 | 43314 | 2300 | 97.25 | 0.17844 | 0.1762 | 0.22018 | RANDOM | 21.477 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-1.79 | -0.16 | 1.95 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.232 |
r_dihedral_angle_4_deg | 22.924 |
r_dihedral_angle_3_deg | 14.38 |
r_dihedral_angle_1_deg | 6.177 |
r_scangle_it | 3.329 |
r_scbond_it | 2.054 |
r_angle_refined_deg | 1.983 |
r_mcangle_it | 1.544 |
r_mcbond_it | 0.876 |
r_mcbond_other | 0.202 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3274 |
Nucleic Acid Atoms | |
Solvent Atoms | 290 |
Heterogen Atoms | 9 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |