6ASD
Zinc finger region of human TET1 in complex with CpG DNA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4HP3 | PDB entry 4hp3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.5 | 291 | 25% PEG-3350, 0.2 M ammonium acetate, 0.1 M HEPES |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 52.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.502 | α = 90 |
b = 31.951 | β = 121.82 |
c = 65.414 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | CCD | ADSC QUANTUM 315r | 2013-06-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97918 | 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 | 1.85 | 36.72 | 98.3 | 0.038 | 0.044 | 0.023 | 1 | 22.1 | 3.6 | 11082 |
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 | 1.85 | 1.89 | 95.7 | 0.423 | 0.494 | 0.252 | 0.872 | 3.8 | 676 |
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 | PDB entry 4hp3 | 1.85 | 36.72 | 10543 | 539 | 98.13 | 0.2033 | 0.2016 | 0.235 | 36.226 |
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] | |
-1.09 | 0.3 | 0.37 | 0.19 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 44.548 |
r_dihedral_angle_3_deg | 12.492 |
r_dihedral_angle_4_deg | 6.978 |
r_dihedral_angle_1_deg | 4.799 |
r_mcangle_it | 1.74 |
r_angle_refined_deg | 1.455 |
r_angle_other_deg | 1.336 |
r_mcbond_it | 1.188 |
r_mcbond_other | 1.187 |
r_chiral_restr | 0.075 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 348 |
Nucleic Acid Atoms | 486 |
Solvent Atoms | 58 |
Heterogen Atoms | 19 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |