4R3H
The crystal structure of an apo RNA binding protein
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 6.5 | 293 | 25% PEG3350, 0.2M Ammonium Sulphate, 0.1M bis-tris, pH 6.5, vapor diffusion, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 45.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.264 | α = 90 |
b = 103.026 | β = 105.86 |
c = 41.585 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | IMAGE PLATE | RIGAKU RAXIS | 2014-03-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
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 | 1.8 | 27.31 | 99.1 | 0.086 | 10.9 | 3.6 | 28931 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.8 | 1.84 | 90.3 | 0.901 | 0.574 | 1.7 | 3.3 | 1528 |
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 | MIR | THROUGHOUT | 1.9 | 25 | 24951 | 1007 | 99.63 | 0.193 | 0.1909 | 0.24 | THIN SHELLS (SFTOOLS) | 32.1817 |
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] | |
0.8 | 0.86 | -1.01 | -0.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.688 |
r_dihedral_angle_4_deg | 16.973 |
r_dihedral_angle_3_deg | 12.366 |
r_dihedral_angle_1_deg | 6.242 |
r_mcangle_it | 2.446 |
r_mcbond_it | 1.634 |
r_mcbond_other | 1.633 |
r_angle_refined_deg | 1.338 |
r_angle_other_deg | 0.761 |
r_chiral_restr | 0.082 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2427 |
Nucleic Acid Atoms | |
Solvent Atoms | 158 |
Heterogen Atoms | 16 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |