7D98
Crystal structure of full-length CbnR complexed with the target DNA complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1IZ1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 293 | 20%(w/v) PEG 3350, 0.5%(w/v) n-Octyl-pyranoside, 4%(v/v) Tacsimate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.99 | 64.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 105.819 | α = 90 |
b = 105.819 | β = 90 |
c = 602.516 | γ = 120 |
Symmetry | |
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Space Group | P 61 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 | 95 | PIXEL | DECTRIS EIGER X 4M | 2016-12-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-1A | 1.9000 | Photon Factory | BL-1A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rpim 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 | 3.6 | 20 | 98.5 | 0.061 | 12 | 13.7 | 23984 | 116.8 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 3.6 | 3.89 | 0.458 | 2.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1IZ1 | 3.6 | 20 | 1.34 | 23960 | 1187 | 98.48 | 0.237 | 0.2344 | 0.2861 | 124.84 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 20.8096 |
f_angle_d | 0.7061 |
f_chiral_restr | 0.0447 |
f_plane_restr | 0.0063 |
f_bond_d | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8088 |
Nucleic Acid Atoms | 1170 |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
XDS | data processing |
Aimless | data scaling |
Coot | model building |
MOLREP | phasing |
PHENIX | refinement |