5HLK
Crystal structure of the ternary EcoRV-DNA-Lu complex with cleaved DNA substrate.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 9.4 mg/mL, 3:3 Enzyme:Well, 100 mM HEPES pH 7.5, 8% Ethylene glycol, 7% Polyethylene glycol 8000, 10% glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.01 | 38.87 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 47.621 | α = 96.94 |
b = 48.327 | β = 108.78 |
c = 63.531 | γ = 106.7 |
Symmetry | |
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Space Group | P 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 | CCD | RIGAKU SATURN 944 | 2014-01-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E DW | 1.54178 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | 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 | 1.95 | 58.46 | 78.9 | 0.051 | 0.057 | 0.995 | 20.3 | 4.3 | 28737 | 2 | 18.6 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.95 | 2 | 12 | 0.238 | 2.7 | 1.6 |
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 | 1B94 | 2 | 40 | 26617 | 1365 | 82.95 | 0.16858 | 0.16553 | 0.22832 | RANDOM | 22.437 |
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] | |
0.37 | -1.03 | -0.79 | 2.48 | -0.25 | -1.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.576 |
r_dihedral_angle_4_deg | 16.997 |
r_dihedral_angle_3_deg | 15.107 |
r_dihedral_angle_1_deg | 6.95 |
r_long_range_B_refined | 6.616 |
r_long_range_B_other | 6.614 |
r_scangle_other | 4.002 |
r_mcangle_it | 3.172 |
r_mcangle_other | 3.171 |
r_scbond_it | 2.463 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4046 |
Nucleic Acid Atoms | 468 |
Solvent Atoms | 237 |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |