5NVG
Thr12 Phosphorylated Ubiquitin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.2 | 291.15 | 20% (v/v) ethanol, 20% (w/v) PEG-1000, 0.1M Phosphate-citrate pH 4.2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.58 | 22.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.46 | α = 90 |
b = 24.74 | β = 113.17 |
c = 47.65 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 PILATUS3 6M | 2017-03-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.97199 | ESRF | ID23-1 |
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 | 1.07 | 43.81 | 95.6 | 0.087 | 7.5 | 2.9 | 22954 |
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 | 1.07 | 1.09 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.07 | 43.81 | 21851 | 1103 | 95.13 | 0.13092 | 0.12905 | 0.16653 | RANDOM | 16.872 |
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] | |
1.1 | -0.36 | -0.84 | 0.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_bonded | 40.109 |
r_sphericity_free | 38.529 |
r_dihedral_angle_2_deg | 30.112 |
r_long_range_B_refined | 19.515 |
r_long_range_B_other | 19.486 |
r_dihedral_angle_3_deg | 15.25 |
r_dihedral_angle_4_deg | 14.835 |
r_dihedral_angle_1_deg | 7.429 |
r_rigid_bond_restr | 7.268 |
r_scangle_other | 4.99 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 602 |
Nucleic Acid Atoms | |
Solvent Atoms | 62 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Coot | model building |
PHASER | phasing |
iMOSFLM | data reduction |
Aimless | data scaling |