7YUN
Crystal structure of human BEND6 BEN domain in complex with methylated DNA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7YUK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 291 | 0.1 M carboxylic acids, 0.1 M imidazole, 0.1 M MES monohydrate (acid) (pH 6.5), 12.5% MPD (v/v), 12.5 % PEG 1000 (v/v), and 12.5% PEG 3350 (w/v). |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.24 | 45.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.482 | α = 90 |
b = 67.276 | β = 100.72 |
c = 53.019 | γ = 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 | Bruker PHOTON III | 2022-05-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | LIQUID ANODE | BRUKER METALJET | 1.34138 |
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 | 2.13 | 34.34 | 99.9 | 0.0559 | 17.36 | 4.77 | 15367 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.13 | 2.16 | 99.8 | 0.2398 | 4.5 | 3.14 |
Refinement
Statistics | |||||||||||||||||||
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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 | 7YUK | 2.13 | 34.34 | 14571 | 780 | 99.94 | 0.18694 | 0.18447 | 0.23356 | RANDOM | 24.344 |
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] | |
0.01 | 0.01 | -0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.461 |
r_dihedral_angle_4_deg | 18.259 |
r_dihedral_angle_3_deg | 15.603 |
r_dihedral_angle_1_deg | 6.66 |
r_long_range_B_refined | 5.429 |
r_long_range_B_other | 5.337 |
r_scangle_other | 3.779 |
r_mcangle_it | 2.799 |
r_mcangle_other | 2.798 |
r_scbond_it | 2.437 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1465 |
Nucleic Acid Atoms | 488 |
Solvent Atoms | 155 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SAINT | data scaling |
SAINT | data reduction |
PDB_EXTRACT | data extraction |
PHASER | phasing |