6RNZ
Crystal structure of the N-terminal HTH DNA-binding domain of the essential repressor DdrO from radiation-resistant Deinococcus bacteria (Deinococcus deserti)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6RNX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.1 M Bis-Tris propane pH 7, 2.5 M Ammonium Sulfate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.42 | 49.14 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.257 | α = 90 |
b = 43.227 | β = 106.66 |
c = 45.87 | 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 | PIXEL | DECTRIS PILATUS3 2M | 2016-07-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-1 | 0.9660 | ESRF | MASSIF-1 |
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 | 1.35 | 44 | 98.3 | 0.048 | 10.9 | 2.8 | 31092 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.35 | 1.4 |
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 | 6RNX | 1.35 | 43.94 | 29520 | 1558 | 98.2 | 0.13114 | 0.1287 | 0.17701 | RANDOM | 16.675 |
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] | |
0.26 | -0.31 | -0.23 | 0.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 38.979 |
r_dihedral_angle_2_deg | 31.905 |
r_dihedral_angle_4_deg | 23.005 |
r_dihedral_angle_3_deg | 13.594 |
r_sphericity_bonded | 12.856 |
r_long_range_B_refined | 6.156 |
r_long_range_B_other | 6.154 |
r_rigid_bond_restr | 5.473 |
r_scangle_other | 4.55 |
r_dihedral_angle_1_deg | 4.242 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1054 |
Nucleic Acid Atoms | |
Solvent Atoms | 255 |
Heterogen Atoms | 18 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
autoPROC | data scaling |
MOLREP | phasing |