4GZ1
Mus Musculus Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex at 1.5 Angstroms resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7 | 293 | 12% PEG 3350, 100mM HEPES, 50mM Mg(CO2)2, pH 7, vapor diffusion, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.2 | α = 90 |
b = 69.139 | β = 90 |
c = 167.789 | 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 | CCD | MAR300 | 2012-06-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.000 | APS | 22-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.5 | 50 | 98.2 | 105967 | 104060 | 2.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | 1.5 | 30.073 | 1.35 | 108008 | 104060 | 5276 | 97.98 | 0.1468 | 0.1453 | 0.1751 | random | 33.7821 |
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] | |
-3.7149 | 3.2334 | 0.4815 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_angle_deg | 1.3 |
f_bond_d | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3984 |
Nucleic Acid Atoms | 368 |
Solvent Atoms | 469 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
DENZO | data reduction |
PHASER | phasing |
SCALEPACK | data scaling |