4FJV
Crystal Structure of Human Otubain2 and Ubiquitin Complex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 279 | 15 % (w/v) Polyethylene Glycol 3350, 0.1 M Magnesium Formate , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 279K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.77 | 55.52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.063 | α = 90 |
b = 76.825 | β = 90 |
c = 198.847 | 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 | PIXEL | DECTRIS PILATUS 2M | 2011-05-12 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 2M | 2011-05-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.9173 | Diamond | I04-1 |
2 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.9173 | Diamond | I04-1 |
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 | 2.047 | 50 | 99.1 | 0.168 | 11 | 9 | 52092 | -1 |
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 | 2.05 | 2.12 | 96.1 | 0.627 | 2.5 | 6.9 | 4955 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1TFF and 3N32 | 2.047 | 49.712 | 52002 | 2641 | 97.65 | 0.2088 | 0.2057 | 0.2672 | RANDOM |
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] | |
-1.9217 | 3.726 | -1.8043 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.912 |
f_angle_d | 1.035 |
f_chiral_restr | 0.075 |
f_bond_d | 0.007 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5086 |
Nucleic Acid Atoms | |
Solvent Atoms | 560 |
Heterogen Atoms | 42 |
Software
Software | |
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Software Name | Purpose |
MOLREP | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |