3G0J
Crystal Structure of the fifth Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3DWY | ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC |
experimental model | PDB | 3DAI | ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC |
experimental model | PDB | 3D7C | ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC |
experimental model | PDB | 2OUO | ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC |
experimental model | PDB | 2OSS | ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC |
experimental model | PDB | 2OO1 | ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC |
experimental model | PDB | 2NXB | ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC |
experimental model | PDB | 2GRC | ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | 0.2M Na_nitrate, 25% w/v PEG 3350, 5% v/v ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.46 | 49.96 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 36.57 | α = 90 |
b = 57.37 | β = 90 |
c = 137.3 | γ = 90 |
Symmetry | |
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Space Group | P 2 21 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 | IMAGE PLATE | RIGAKU RAXIS IV | 2008-12-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E SUPERBRIGHT | 1.5 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.78 | 30.831 | 98.9 | 0.079 | 0.079 | 18.2 | 8.8 | 28619 | 28304 | 22.8 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.78 | 1.88 | 100 | 0.703 | 0.703 | 2.6 | 9 | 4085 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC | 1.78 | 29.45 | 28246 | 1428 | 98.84 | 0.193 | 0.193 | 0.19 | 0.237 | RANDOM | 15.392 |
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] | |
0.45 | -0.29 | -0.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.468 |
r_dihedral_angle_3_deg | 14.478 |
r_dihedral_angle_4_deg | 13.52 |
r_scangle_it | 6.667 |
r_scbond_it | 5.21 |
r_dihedral_angle_1_deg | 5.187 |
r_mcangle_it | 3.557 |
r_mcbond_it | 2.808 |
r_angle_refined_deg | 1.373 |
r_mcbond_other | 1.266 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1870 |
Nucleic Acid Atoms | |
Solvent Atoms | 263 |
Heterogen Atoms | 20 |
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 |