2XCA
TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, 7,8- DIHYDRO-8-OXODEOXYGUANINE MODIFIED DNA AND dGTP - MAGNESIUM FORM
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2C22 | PDB ENTRY 2C22 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | RESERVOIR: 12-20% POLYETHYLENE GLYCOL 3350, 0.2 M AMMONIUM ACETATE, 0.1 M MAGNESIUM ACETATE, 20 MM TRIS (PH 7.5) DROP: 10MM TRIS-CL PH 7.5, 30 MM NACL, 0.5MM DGTP, 2.5MM MGCL2, 6-10% POLYETHYLENE GLYCOL 3350 0.1M AMMONIUM ACETATE, 0.05M MAGNESIUM ACETATE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.23 | 50.09 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 94.443 | ¦Á = 90 |
b = 103.909 | ¦Â = 90 |
c = 52.707 | ¦Ã = 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 | 2007-02-05 | 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 | 2.5 | 29.13 | 99.6 | 0.06 | 21.3 | 5.8 | 18457 | 1 | 46.9 |
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 | 2.5 | 2.66 | 99.9 | 0.49 | 4.2 | 5.3 |
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 2C22 | 2.5 | 29.13 | 18457 | 900 | 99.6 | 0.22 | 0.22 | 0.259 | RANDOM | 44.1 |
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] | |
4.73 | -0.9 | -3.82 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.6 |
c_scangle_it | 3.01 |
c_mcangle_it | 2.24 |
c_scbond_it | 1.93 |
c_improper_angle_d | 1.55 |
c_angle_deg | 1.4 |
c_mcbond_it | 1.34 |
c_bond_d | 0.008 |
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 | 192 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
XDS | data reduction |
XDS | data scaling |
CNS | phasing |