7B1Y
DtxR-like iron-dependent regulator IdeR complexed with cobalt and its consensus DNA-binding sequence
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 293 | 30%(w/v) PEG 2000 MME, 0.2 M ammonium sulfate, 0.1 M sodium acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.58 | 65.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 195.035 | α = 90 |
b = 112.899 | β = 117.07 |
c = 88.505 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 EIGER X 16M | 2020-04-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX IV BEAMLINE BioMAX | 0.97624 | MAX IV | BioMAX |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 2.12 | 78.94 | 92.5 | 0.092 | 0.099 | 0.038 | 0.997 | 11.2 | 6.9 | 60545 |
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) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.12 | 2.32 | 59 | 1.203 | 1.304 | 0.497 | 0.581 | 1.7 | 6.7 |
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 | 7B1V | 2.12 | 78.94 | 57538 | 3007 | 62.77 | 0.2308 | 0.2297 | 0.2526 | RANDOM | 50.015 |
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] | |
0.12 | 0.07 | 0.15 | -0.22 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 26.334 |
r_dihedral_angle_4_deg | 16.038 |
r_dihedral_angle_3_deg | 12.691 |
r_dihedral_angle_1_deg | 4.95 |
r_angle_refined_deg | 1.1 |
r_angle_other_deg | 1.078 |
r_chiral_restr | 0.038 |
r_bond_refined_d | 0.002 |
r_gen_planes_refined | 0.002 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7002 |
Nucleic Acid Atoms | 1189 |
Solvent Atoms | 136 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |