5CXT
Crystal structure of a RNA-binding protein 39 (RBM39) in complex with fragment of splicing factor (U2AF) from Unknown at 2.20 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3S6E |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 277 | 0.1M potassium chloride, 15.0% polyethylene glycol monomethyl ether 5000, 0.1M HEPES pH 7.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.55 | 51.79 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 127.283 | α = 90 |
b = 127.283 | β = 90 |
c = 78.864 | γ = 120 |
Symmetry | |
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Space Group | P 32 |
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 | MARMOSAIC 325 mm CCD | Vertical focusing mirror; double crystal Si(111) monochromator | 2013-11-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL14-1 | 1.0 | SSRL | BL14-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 39.432 | 99.7 | 0.116 | 0.135 | 9.71 | 3.809 | 72455 | -3 | 34.1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.2 | 2.26 | 98 | 0.83 | 0.981 | 2 |
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 | 3S6E | 2.2 | 39.432 | 72263 | 3629 | 99.68 | 0.1751 | 0.1744 | 0.1897 | RANDOM | 39.3644 |
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] | |
8.73 | 8.73 | -17.47 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.92 |
r_dihedral_angle_4_deg | 18.357 |
r_dihedral_angle_3_deg | 12.274 |
r_dihedral_angle_1_deg | 5.2 |
r_mcangle_it | 3.713 |
r_mcbond_it | 2.282 |
r_mcbond_other | 2.28 |
r_angle_refined_deg | 1.635 |
r_angle_other_deg | 1.493 |
r_chiral_restr | 0.101 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8553 |
Nucleic Acid Atoms | |
Solvent Atoms | 518 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
REFMAC | refinement |
PHASER | phasing |