6D1T
Complex of MBD1-MBD and methylated DNA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6CC8 | earlier version of PDB entry 6cc8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 291 | 30% PEG-550-MME, 0.1 M magnesium chloride, 0.1 M HEPES |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 49.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 28.574 | α = 90 |
b = 74.193 | β = 90 |
c = 138.872 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | ADSC QUANTUM 315 | 2012-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97911 | APS | 19-ID |
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 | 2.25 | 46.29 | 99.9 | 0.056 | 0.061 | 0.023 | 0.999 | 20.3 | 6.9 | 7412 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.25 | 2.32 | 100 | 1.083 | 1.167 | 0.43 | 0.641 | 7.2 | 674 |
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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | earlier version of PDB entry 6cc8 | 2.25 | 37.1 | 6633 | 748 | 99.81 | 0.2382 | 0.2349 | 0.2693 | 51.071 |
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] | |
0.5 | -0.77 | 0.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_4_deg | 26.124 |
r_dihedral_angle_2_deg | 17.132 |
r_dihedral_angle_3_deg | 16.784 |
r_dihedral_angle_1_deg | 6.121 |
r_mcangle_it | 2.294 |
r_angle_refined_deg | 1.533 |
r_mcbond_it | 1.416 |
r_mcbond_other | 1.414 |
r_angle_other_deg | 0.991 |
r_chiral_restr | 0.075 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 527 |
Nucleic Acid Atoms | 488 |
Solvent Atoms | |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |