2UVV
Crystal structures of mutant Dpo4 DNA polymerases with 8-oxoG containing DNA template-primer constructs
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2UVR | PDB ENTRY 2UVR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.3 | 7% PEG 4000, 10 MM HEPES PH 7.3, 50 MM CA(CH3CO2)2, 50MM NACL, 3.5% GLYCEROL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 55.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 95.776 | α = 90 |
b = 103.725 | β = 90 |
c = 53.032 | 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 | 2006-12-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 5ID-B | APS | 5ID-B |
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 | 2.2 | 29.32 | 99.1 | 0.05 | 23.61 | 6.38 | 27480 | 1 | 43.2 |
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 | 2.2 | 2.28 | 98.6 | 0.44 | 4.41 | 6.57 |
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 2UVR | 2.2 | 29.32 | 27480 | 1345 | 99.7 | 0.228 | 0.228 | 0.257 | RANDOM | 40.3 |
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] | |
-1.12 | -1.68 | 2.8 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.3 |
c_scangle_it | 2.95 |
c_mcangle_it | 2.24 |
c_scbond_it | 1.97 |
c_improper_angle_d | 1.48 |
c_mcbond_it | 1.37 |
c_angle_deg | 1.3 |
c_bond_d | 0.007 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2751 |
Nucleic Acid Atoms | 592 |
Solvent Atoms | 182 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
XDS | data reduction |
XDS | data scaling |
CNS | phasing |