4RQ4
Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine(8-oxoG) and dATP soaked with MgCl2 for 30 s
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 295 | 50 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.12 | 41.93 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 49.16 | ¦Á = 90 |
b = 79.65 | ¦Â = 106.35 |
c = 55.31 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 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 | RAYONIX MX225HE | 2014-07-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.97931 | APS | 31-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 | 2.1 | 40.59 | 99.7 | 0.076 | 7.8 | 3.2 | 23899 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.1 | 2.16 | 99.8 | 0.382 | 2.5 | 3.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.1 | 40.59 | 22700 | 1180 | 99.67 | 0.1923 | 0.18961 | 0.24363 | RANDOM | 34.463 |
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] | |
0.04 | -0.03 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.096 |
r_dihedral_angle_3_deg | 14.621 |
r_dihedral_angle_4_deg | 10.642 |
r_long_range_B_refined | 5.721 |
r_long_range_B_other | 5.721 |
r_dihedral_angle_1_deg | 5.647 |
r_scangle_other | 3.765 |
r_mcangle_it | 3.007 |
r_mcangle_other | 3.007 |
r_scbond_it | 2.298 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2613 |
Nucleic Acid Atoms | 654 |
Solvent Atoms | 195 |
Heterogen Atoms | 53 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALEPACK | data scaling |