3GG3
Crystal Structure of the Bromodomain of Human PCAF
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2NXB | PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI |
experimental model | PDB | 2OO1 | PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI |
experimental model | PDB | 2OSS | PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI |
experimental model | PDB | 2OUO | PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI |
experimental model | PDB | 2RFJ | PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI |
experimental model | PDB | 3DAI | PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.2 | 277 | 20% PEG10K, 4% Ethylene Glycol, 0.1M HEPES pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.38 | 63.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 99.226 | α = 90 |
b = 99.226 | β = 90 |
c = 101.137 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS IV | 2008-07-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E SUPERBRIGHT | 1.5 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.25 | 32.743 | 100 | 0.048 | 0.048 | 12.5 | 2.8 | 17604 | 17604 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.25 | 2.37 | 100 | 0.456 | 0.456 | 2 | 2.8 | 2567 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI | 2.25 | 32.74 | 17610 | 17594 | 892 | 99.91 | 0.209 | 0.209 | 0.207 | 0.245 | RANDOM | 31.265 |
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] | |
-0.66 | -0.33 | -0.66 | 1 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.425 |
r_dihedral_angle_4_deg | 22.367 |
r_dihedral_angle_3_deg | 14.16 |
r_scangle_it | 11.709 |
r_scbond_it | 9.302 |
r_dihedral_angle_1_deg | 5.605 |
r_mcangle_it | 5.521 |
r_mcbond_it | 3.906 |
r_angle_refined_deg | 1.42 |
r_mcbond_other | 1.25 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1728 |
Nucleic Acid Atoms | |
Solvent Atoms | 120 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrystalClear | data collection |
MOSFLM | data reduction |