5HNK
Crystal structure of T5Fen in complex intact substrate and metal ions.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 290 | The concentration of both oligonucleotides was adjusted to 1.1 mM for the duplex molecule by dissolving each one in 10 mM MES pH 6.5 and 50 mM KCl. They were annealed by heating to 367K for 10 minutes and allowed to cool to room temperature. Crystals with oligonucleotide 5ov4 were grown at 290K with the D153K variant of T5Fen. The resulting T5FenD153K:5ov4 structure was determined from crystals grown in 0.2 M MgCl2, 0.1 M Bis-Tris buffer pH 5.5, 25% w/v PEG 3350. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.24 | 45.06 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.72 | α = 90 |
b = 109.94 | β = 90 |
c = 127.34 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | Please check which detector was in place at that date | 2011-04-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.977 | Diamond | I24 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.22 | 44.72 | 99.4 | 0.079 | 0.094 | 0.038 | 13.4 | 5.7 | 31727 | 31727 |
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) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.22 | 2.28 | 94.8 | 0.654 | 0.654 | 0.405 | 0.9 | 3.1 | 2177 |
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 | 1EXN | 2.22 | 42.19 | 30073 | 1595 | 99.35 | 0.1851 | 0.1826 | 0.2344 | RANDOM | 48.335 |
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] | |
-0.17 | -0.46 | 0.63 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.873 |
r_dihedral_angle_3_deg | 11.925 |
r_dihedral_angle_4_deg | 11.084 |
r_dihedral_angle_1_deg | 5.305 |
r_mcangle_it | 3.997 |
r_mcbond_it | 2.659 |
r_mcbond_other | 2.659 |
r_angle_refined_deg | 1.066 |
r_angle_other_deg | 0.947 |
r_chiral_restr | 0.065 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4407 |
Nucleic Acid Atoms | 490 |
Solvent Atoms | 224 |
Heterogen Atoms | 9 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
xia2 | data reduction |
PHASER | phasing |