1LJM
DNA recognition is mediated by conformational transition and by DNA bending
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1E50 | PDB ENTRY 1E50 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 292 | Ethanol, Sodium Chloride, Tris-HCl, Hepes, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.52 | 72.76 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 121.23 | α = 90 |
b = 121.23 | β = 90 |
c = 186.33 | γ = 120 |
Symmetry | |
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Space Group | H 3 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 | IMAGE PLATE | RIGAKU RAXIS IV | mirrors | 2000-01-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU ULTRAX 18 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.5 | 43 | 99.3 | 0.071 | 0.071 | 17.2 | 13.9 | 17501 | 17379 | -3 | 31.5 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.5 | 2.54 | 99.3 | 0.295 | 0.295 | 2.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1E50 | 2.5 | 43 | 17501 | 17379 | 842 | 99.3 | 0.1947 | 0.1947 | 0.193 | 0.249 | RANDOM | 40.5 |
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 | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 26.5 |
c_scbond_it | 3.8 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.78 |
c_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1759 |
Nucleic Acid Atoms | |
Solvent Atoms | 201 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
MTF/ULTIMA | model building |
CNS | refinement |
MTF | phasing |
ULTIMA | phasing |