2C2R
Efficient and High Fidelity Incorporation of dCTP Opposite 7,8- Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2C28 | PDB ENTRY 2C28 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 5% PEG 3350,0.010 M TRIS-HCL PH 7.5, 100 MM CA(CH3CO2)2, 1.25% GLYCEROL, 30 MM NACL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 51.05 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 95.2 | α = 90 |
b = 100.15 | β = 90 |
c = 52 | 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 | ADSC CCD | 2005-08-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | APS | 17-ID |
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 | 2.55 | 42.99 | 98.8 | 0.12 | 8.77 | 3.64 | 16653 | 1 | 55.1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.55 | 2.71 | 93.9 |
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 2C28 | 2.55 | 42.99 | 16645 | 817 | 98.8 | 0.251 | 0.251 | 0.31 | RANDOM | 54.6 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
27.67 | -18.88 | -8.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.3 |
c_scangle_it | 2.65 |
c_mcangle_it | 2.23 |
c_scbond_it | 1.71 |
c_improper_angle_d | 1.43 |
c_angle_deg | 1.4 |
c_mcbond_it | 1.29 |
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 | 2744 |
Nucleic Acid Atoms | 608 |
Solvent Atoms | 106 |
Heterogen Atoms | 31 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |