2W8K
Y-family DNA polymerase Dpo4 bypassing N2-naphthyl-guanine adduct in syn orientation
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | DPO4:DNA COMPLEX (1:1.2 MOLAR RATIO; 150 MICROMOLAR), 20 MM TRIS HCL (PH 7.4), 15% POLYETHYLENE GLYCOL 3350 (W/V), 60 MM SODIUM CHLORIDE, 5 MM MAGNESIUM CHLORIDE, 4% GLYCEROL, 1 MM DGTP. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 56.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 95.04 | α = 90 |
b = 103.91 | β = 90 |
c = 52.32 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 110 | CCD | MARRESEARCH | MIRRORS | 2008-06-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | APS | 21-ID-F |
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 | 3.1 | 30 | 98.4 | 0.09 | 15.6 | 6 | 9733 | 62.4 |
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 | 3.1 | 3.2 | 95.1 | 0.65 | 3.2 | 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 | PDB ENTRY 2BQR | 3.1 | 19.97 | 9806 | 521 | 99.5 | 0.233 | 0.233 | 0.282 | RANDOM | 88.9 |
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] | |
17.16 | -19.92 | 2.77 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.8 |
c_scangle_it | 2.57 |
c_mcangle_it | 2.24 |
c_improper_angle_d | 1.96 |
c_angle_deg | 1.6 |
c_scbond_it | 1.53 |
c_mcbond_it | 1.25 |
c_bond_d | 0.009 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2754 |
Nucleic Acid Atoms | 613 |
Solvent Atoms | 80 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
XDS | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |