8XK7
binary complex of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 289 | 0.2 M lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, and 28% PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.94 | 58.19 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 61.61 | ¦Á = 90 |
b = 65.628 | ¦Â = 103.51 |
c = 107.378 | ¦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 | 100 | PIXEL | DECTRIS PILATUS3 6M | 2021-12-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL18U1 | 0.979 | SSRF | BL18U1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 50 | 98.8 | 0.135 | 0.148 | 0.06 | 0.974 | 4.3 | 6.1 | 55909 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2 | 2.03 | 99.7 | 0.586 | 0.64 | 0.255 | 0.915 | 6.3 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2 | 24.41 | 53014 | 2832 | 98.77 | 0.19347 | 0.19151 | 0.2012 | 0.2311 | 0.2324 | RANDOM | 36.354 |
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] | |
1.66 | -1.33 | 3.74 | -4.27 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 15.286 |
r_dihedral_angle_2_deg | 12.959 |
r_long_range_B_refined | 5.957 |
r_long_range_B_other | 5.957 |
r_dihedral_angle_1_deg | 5.837 |
r_scangle_other | 4.326 |
r_mcangle_other | 3.294 |
r_mcangle_it | 3.293 |
r_scbond_it | 2.843 |
r_scbond_other | 2.842 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4315 |
Nucleic Acid Atoms | 619 |
Solvent Atoms | 346 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALEPACK | data scaling |
HKL-3000 | data reduction |
PHASER | phasing |