3RAQ
Dpo4 extension ternary complex with 3'-terminal primer C base opposite the 1-methylguanine (MG1) lesion
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 100 mM HEPES, pH 7.0, 100 mM calcium acetate and 10% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.89 | 57.37 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.194 | α = 98.97 |
b = 62.077 | β = 103.82 |
c = 91.459 | γ = 93.72 |
Symmetry | |
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Space Group | P 1 |
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 | CCD | ADSC QUANTUM 315 | 2006-07-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.97949 | APS | 24-ID-C |
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 | 2.25 | 20 | 98.4 | 0.107 | 3.6 | 51859 | 2 |
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 | 2.25 | 2.31 | 96.8 | 2 | 2.8 | 3622 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | 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 3GIJ | 2.25 | 20 | 2 | 51859 | 48438 | 2578 | 98.27 | 0.19589 | 0.19379 | 0.23505 | RANDOM | 44.889 |
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] | |
-2.05 | 0.06 | -0.32 | 0.05 | -0.05 | 1.84 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.672 |
r_dihedral_angle_4_deg | 18.619 |
r_dihedral_angle_3_deg | 14.87 |
r_dihedral_angle_1_deg | 5.2 |
r_scangle_it | 2.04 |
r_angle_refined_deg | 1.42 |
r_scbond_it | 1.259 |
r_angle_other_deg | 0.895 |
r_mcangle_it | 0.883 |
r_mcbond_it | 0.523 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5480 |
Nucleic Acid Atoms | 1237 |
Solvent Atoms | 298 |
Heterogen Atoms | 98 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
AMoRE | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |