5MN9
Crystal structure of MINDY-1 tMIU in complex with K48-diUb
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.4 | 293.15 | 100 mM sodium acetate pH 5.4 and 18.5 % PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.82 | 32.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.14 | α = 90 |
b = 55.14 | β = 90 |
c = 105.51 | γ = 90 |
Symmetry | |
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Space Group | I 41 |
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 2M | 2015-05-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-1 | 0.96769 | ESRF | MASSIF-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.05 | 48.87 | 100 | 0.043 | 0.999 | 19.4 | 6.6 | 9899 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.05 | 2.11 | 100 | 0.544 | 0.818 | 2.9 | 6.6 |
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 | 1UBQ | 2.05 | 48.87 | 9368 | 517 | 99.97 | 0.18484 | 0.18268 | 0.22341 | RANDOM | 58.638 |
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] | |
0.34 | 0.34 | -0.69 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.29 |
r_dihedral_angle_3_deg | 14.185 |
r_dihedral_angle_4_deg | 13.893 |
r_long_range_B_other | 7.313 |
r_long_range_B_refined | 7.303 |
r_scangle_other | 6.165 |
r_dihedral_angle_1_deg | 6.1 |
r_scbond_it | 3.95 |
r_scbond_other | 3.947 |
r_mcangle_other | 3.808 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1332 |
Nucleic Acid Atoms | |
Solvent Atoms | 3 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
PHASER | phasing |
REFMAC | refinement |
XDS | data scaling |