6IPE
Post-catalytic Complex of Human DNA Polymerase Mu with Templating Adenine and Mg-8oxodGMP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | 0.1 M HEPES pH 7.5, 18% PEG 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.49 | 50.53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.889 | α = 90 |
b = 68.402 | β = 90 |
c = 110.512 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 100 | CCD | RAYONIX MX300-HS | 2018-04-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSRRC BEAMLINE TPS 05A | 1 | NSRRC | TPS 05A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.69 | 30 | 99.8 | 0.05 | 0.019 | 40.57 | 7 | 50902 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.69 | 1.75 | 99.1 | 0.803 | 0.329 | 2.2 | 5.6 |
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 | 1.7 | 30 | 47243 | 2538 | 97.41 | 0.17437 | 0.17279 | 0.20364 | RANDOM | 16.574 |
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] | |
-0.12 | 0.1 | 0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.802 |
r_dihedral_angle_4_deg | 18.463 |
r_dihedral_angle_3_deg | 12.236 |
r_dihedral_angle_1_deg | 4.988 |
r_long_range_B_refined | 4.83 |
r_long_range_B_other | 4.829 |
r_scangle_other | 1.793 |
r_mcangle_it | 1.771 |
r_mcangle_other | 1.77 |
r_angle_refined_deg | 1.363 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2561 |
Nucleic Acid Atoms | 367 |
Solvent Atoms | 434 |
Heterogen Atoms | 30 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |