6FGE
Crystal structure of human ZUFSP/ZUP1 in complex with ubiquitin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 293 | 4% v/v Tacsimate pH 5.0 and 12% w/v Polyethylene glycol 3,350. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.75 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 84.484 | α = 90 |
b = 84.484 | β = 90 |
c = 201.867 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 2 |
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 6M-F | Compound Refractive Lenses | 2017-07-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.91587 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | 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 | 1.74 | 100.93 | 100 | 0.082 | 0.085 | 1 | 25.8 | 29 | 44699 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.74 | 1.78 | 100 | 0.99 | 1.02 | 0.93 | 4 | 30.6 |
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 | 73.16 | 42293 | 2308 | 100 | 0.17538 | 0.17353 | 0.20944 | RANDOM | 35.096 |
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] | |
-0.1 | -0.05 | -0.1 | 0.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.477 |
r_dihedral_angle_4_deg | 16.491 |
r_dihedral_angle_3_deg | 13.342 |
r_long_range_B_refined | 8.067 |
r_long_range_B_other | 8.063 |
r_dihedral_angle_1_deg | 6.588 |
r_scangle_other | 6.061 |
r_scbond_it | 4.275 |
r_scbond_other | 4.266 |
r_mcangle_it | 3.588 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3308 |
Nucleic Acid Atoms | |
Solvent Atoms | 196 |
Heterogen Atoms | 69 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XDS | data scaling |
REFMAC | refinement |