2H1E
Tandem chromodomains of budding yeast CHD1
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2B2Y | PDB ENTRY 2B2Y, CHAIN A WITHOUT B1-B2 LOOP |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 8 | 283 | 10mM BTP, 12mM NaCl, 5mM TCEP, 0.9M ammonium sulfate, 3.75% isopropanol, 4.5mg/ml yeast CHD1 tandem chromodomains, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.11 | 60.43 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 136.185 | ¦Á = 90 |
b = 136.185 | ¦Â = 90 |
c = 57.516 | ¦Ã = 90 |
Symmetry | |
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Space Group | I 41 |
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 | MARRESEARCH | 2005-07-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | APS | 22-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.2 | 19.57 | 95.7 | 0.104 | 10.8 | 3.5 | 25838 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.2 | 2.28 | 80.9 | 0.449 | 1.7 | 2 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | PDB ENTRY 2B2Y, CHAIN A WITHOUT B1-B2 LOOP | 2.2 | 19.57 | 25934 | 25796 | 1299 | 95.7 | 0.192 | 0.189 | 0.246 | RANDOM | 30.85 |
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] | |
0.01 | 0.01 | -0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.941 |
r_dihedral_angle_1_deg | 28.126 |
r_dihedral_angle_4_deg | 20.282 |
r_dihedral_angle_3_deg | 17.408 |
r_scangle_it | 6.189 |
r_scbond_it | 4.383 |
r_mcangle_it | 2.338 |
r_mcbond_it | 2.25 |
r_angle_refined_deg | 2.226 |
r_nbtor_refined | 0.318 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2740 |
Nucleic Acid Atoms | |
Solvent Atoms | 194 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |