2XC9
BINARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE AND 1, N2-ETHENOGUANINE MODIFIED DNA, MAGNESIUM FORM
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BQ3 | PDB ENTRY 2BQ3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 12-20% POLYETHYLENE GLYCOL 3350, 0.2 M AMMONIUM ACETATE, 0.1 M MAGNESIUM ACETATE, AND 20 MM TRIS (PH 7.5) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.16 | 48.08 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 93.722 | ¦Á = 90 |
b = 102.125 | ¦Â = 90 |
c = 53.004 | ¦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 | ROSENBAUM-ROCK MONOCHROMATOR HIGH -RESOLUTION DOUBLE-CRYSTAL SI (111) SAGITTAL FOCUSING. ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR | 2006-03-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-BM | APS | 22-BM |
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 | 26.91 | 99.3 | 0.06 | 36.3 | 12.6 | 26245 | 1 | 43.4 |
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 | 2.2 | 2.28 | 99.3 | 0.48 | 6.2 | 10.4 |
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 2BQ3 | 2.2 | 26.91 | 26245 | 1270 | 99.2 | 0.221 | 0.221 | 0.25 | RANDOM | 40.7 |
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] | |
6.44 | -2.43 | -4.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.3 |
c_scangle_it | 3.19 |
c_mcangle_it | 2.32 |
c_scbond_it | 2.07 |
c_angle_deg | 1.6 |
c_mcbond_it | 1.42 |
c_improper_angle_d | 1.08 |
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 | 2744 |
Nucleic Acid Atoms | 617 |
Solvent Atoms | 247 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |