3SQ5
Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase H432N Mutant
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.8 | 291 | 20% PEG3350, 0.1M HEPES, 0.2M magnesium sulfate, 5mM TCEP, 3% Hexanediol-1,6, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.453 | α = 89.8 |
b = 82.036 | β = 94.33 |
c = 98.677 | γ = 112.78 |
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 | 200 | CCD | MARMOSAIC 225 mm CCD | 2008-07-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-BM | APS | 22-BM |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.3 | 50 | 92.8 | 0.071 | 13.8 | 3.2 | 75956 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.3 | 2.38 | 97.3 | 0.241 | 3.2 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1Q32 | 2.3 | 50 | 75448 | 75448 | 3872 | 96.1 | 0.204 | 0.203 | 0.236 | RANDOM | 53.87 |
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] | |
0.93 | -0.97 | 1.22 | -2.32 | -1.26 | 0.83 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.846 |
r_dihedral_angle_4_deg | 17.958 |
r_dihedral_angle_3_deg | 16.404 |
r_dihedral_angle_1_deg | 7.013 |
r_scangle_it | 4.535 |
r_scbond_it | 2.823 |
r_angle_refined_deg | 1.907 |
r_mcangle_it | 1.818 |
r_mcbond_it | 0.961 |
r_chiral_restr | 0.134 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13657 |
Nucleic Acid Atoms | |
Solvent Atoms | 125 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |