4R2A
Egr1/Zif268 zinc fingers 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 | 1AAY | PDB entry 1AAY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 289 | 12% (v/v) PEG 3350, 4% Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.38 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 43.99 | ¦Á = 90 |
b = 56.208 | ¦Â = 90 |
c = 130.219 | ¦Ã = 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 | MARMOSAIC 225 mm CCD | 2013-10-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-BM | 1.0000 | APS | 22-BM |
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 | 1.59 | 28.104 | 99.1 | 0.053 | 28.895 | 7.3 | 21919 | -3 | 17.9 |
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 | 1.59 | 1.65 | 95.8 | 0.386 | 3.6 | 5.6 | 2098 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB entry 1AAY | 1.591 | 28.104 | 1.36 | 21919 | 1096 | 98.99 | 0.1399 | 0.1399 | 0.1371 | 0.189 | RANDOM |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 24.642 |
f_angle_d | 1.491 |
f_chiral_restr | 0.066 |
f_bond_d | 0.012 |
f_plane_restr | 0.01 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 707 |
Nucleic Acid Atoms | 447 |
Solvent Atoms | 182 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHENIX | model building |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHENIX | phasing |