2JEG
The Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine by Sulfolobus solfataricus DNA Polymerase IV: Steady-state and Pre-steady-state Kinetics and X- Ray Crystallography of Correct and Incorrect Pairing
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2J6U | PDB ENTRY 2J6U |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.4 | 298 | 10% POLYETHYLENE GLYCOL (W/V), 100 MM CALCIUM ACETATE, 25 MM TRIS HCL PH 7.4, 50 MM NACL, 5 MM CALCIUM CHLORIDE, 1 MM DGTP, 2.5% GLYCEROL (V/V), AT 25 DEGREES CELSIUS. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 50.46 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 93.102 | ¦Á = 90 |
b = 103.165 | ¦Â = 90 |
c = 52.632 | ¦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 | 2006-11-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | APS | 22-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 | 2.38 | 46.55 | 98.7 | 0.1 | 25.5 | 7 | 20833 | 52.2 |
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 | 2.38 | 2.52 | 93.2 | 0.67 | 2.2 | 6.5 |
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 2J6U | 2.38 | 46.55 | 20833 | 1007 | 98.7 | 0.226 | 0.226 | 0.263 | RANDOM | 48.5 |
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] | |
8.35 | -1.23 | -7.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.2 |
c_scangle_it | 3.46 |
c_improper_angle_d | 2.86 |
c_mcangle_it | 2.25 |
c_scbond_it | 2.18 |
c_angle_deg | 1.4 |
c_mcbond_it | 1.37 |
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 | 2754 |
Nucleic Acid Atoms | 633 |
Solvent Atoms | 104 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
CNS | phasing |