6JUS
MsDpo4-DNA complex 6
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6JUL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 295 | PEG 2KMME 12%, Bis Tris Propane pH 6.0, NaCl 0.2 mM |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.88 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 53.73 | ¦Á = 90 |
b = 80.34 | ¦Â = 90 |
c = 208.72 | ¦Ã = 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 | MARMOSAIC 300 mm CCD | 2016-04-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.9786 | ESRF | BM14 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.5 | 44.6 | 99 | 0.084 | 0.042 | 10.9 | 4.9 | 31909 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.5 | 2.64 | 95.3 | 0.552 | 0.268 | 4.9 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 6JUL | 2.5 | 44.6 | 30229 | 1618 | 98.85 | 0.20794 | 0.20551 | 0.25425 | RANDOM | 57.115 |
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] | |
-0.3 | -3.09 | 3.39 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.034 |
r_dihedral_angle_3_deg | 18.967 |
r_dihedral_angle_4_deg | 16.998 |
r_long_range_B_refined | 8.332 |
r_dihedral_angle_1_deg | 7.499 |
r_mcangle_it | 4.281 |
r_scbond_it | 3.672 |
r_mcbond_it | 2.706 |
r_angle_refined_deg | 2.233 |
r_chiral_restr | 0.129 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5290 |
Nucleic Acid Atoms | 877 |
Solvent Atoms | 89 |
Heterogen Atoms | 62 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
Coot | model building |
PHASER | phasing |