2B2V
Crystal structure analysis of human CHD1 chromodomains 1 and 2 bound to histone H3 resi 1-15 MeK4
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2B2T | WITHOUT CHAIN D |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 8 | 283 | 4% PEG3350, 0.05M HEPES, pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 49 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 112.255 | ¦Á = 90 |
b = 54.177 | ¦Â = 111.97 |
c = 99.96 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARRESEARCH | 2005-02-08 | 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 | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.5 | 30.9 | 94.8 | 0.085 | 16.3 | 3.6 | 18233 |
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 | 2.5 | 2.59 | 71.7 | 0.485 | 1.35 | 2.5 |
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 B2T WITHOUT CHAIN D | 2.65 | 30.9 | 18233 | 16146 | 789 | 98.1 | 0.216 | 0.213 | 0.266 | RANDOM | 48.77 |
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] | |
-6.68 | -2.7 | 6.29 | -1.63 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.948 |
r_dihedral_angle_4_deg | 24.459 |
r_dihedral_angle_3_deg | 22.463 |
r_dihedral_angle_1_deg | 8.686 |
r_scangle_it | 7.51 |
r_scbond_it | 5.574 |
r_mcangle_it | 3.56 |
r_mcbond_it | 2.636 |
r_angle_refined_deg | 1.709 |
r_angle_other_deg | 1.107 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3556 |
Nucleic Acid Atoms | |
Solvent Atoms | 123 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
HKL-2000 | data scaling |
MOLREP | phasing |