8R7Y
Deoxyribonucleoside regulator DeoR in complex with the DNA operator
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.3 | 292 | The volume ratio of the protein/DNA solution and precipitant solution - 1:2 Precipitant solution: 50 mM sodium cacodylate, pH 6.3, 75 mM CaCl2, 25 mM MgCl2, 3.5% (v/v) PEG 2K Crystal was cryo-protected by a quick soaking in 25% (v/v) glycerol. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.22 | 70.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 166.672 | α = 90 |
b = 166.672 | β = 90 |
c = 331.697 | γ = 120 |
Symmetry | |
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Space Group | P 65 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 | 100 | PIXEL | DECTRIS PILATUS 6M | 2018-01-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.9141 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim I (All) | 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 | 3.6 | 50 | 98.9 | 0.748 | 0.993 | 4.86 | 13.1 | 32081 | 122.8 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.6 | 3.81 | 96.4 | 8.886 | 0.123 | 0.35 |
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 (All) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3.7 | 48.924 | 29634 | 1482 | 99.2 | 0.269 | 0.2655 | 0.3328 | 172.198 |
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] | |
1.194 | 0.597 | 1.194 | -3.873 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_lrange_it | 36.36 |
r_scangle_it | 25.467 |
r_mcangle_it | 22.766 |
r_dihedral_angle_1_deg | 20.224 |
r_dihedral_angle_3_deg | 17.127 |
r_scbond_it | 15.775 |
r_dihedral_angle_6_deg | 15.735 |
r_mcbond_it | 14.012 |
r_dihedral_angle_2_deg | 5.901 |
r_paralell_plane_angle_deg | 4.846 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9792 |
Nucleic Acid Atoms | 1464 |
Solvent Atoms | 8 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
MOLREP | phasing |