5II2
Crystal Structure of the fifth bromodomain of human polybromo (PB1) in complex with 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3MB4 | Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY |
experimental model | PDB | 3DAI | Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY |
experimental model | PDB | 3HMH | Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY |
experimental model | PDB | 2GRC | Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY |
experimental model | PDB | 2OSS | Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY |
experimental model | PDB | 2OUO | Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY |
experimental model | PDB | 3D7C | Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY |
experimental model | PDB | 3DWY | Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | 0.20M K3(cit) 0.1M BTProp pH 7.5 20.0% PEG 3350 10.0% EtGly |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.87 | 57.08 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.52 | α = 90 |
b = 58.51 | β = 90 |
c = 138.23 | γ = 90 |
Symmetry | |
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Space Group | P 21 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 | 2011-04-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E SUPERBRIGHT | 1.52 |
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 | 2.1 | 24.186 | 99 | 0.127 | 0.127 | 9.1 | 6.3 | 20237 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.1 | 2.21 | 95.3 | 0.368 | 2 | 5.9 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY | 2.1 | 24.186 | 19140 | 1042 | 98.9 | 0.1762 | 0.1735 | 0.2267 | RANDOM | 28.073 |
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] | |
0.56 | 0.67 | -1.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.613 |
r_dihedral_angle_3_deg | 14.346 |
r_dihedral_angle_4_deg | 13.696 |
r_dihedral_angle_1_deg | 5.46 |
r_mcangle_it | 3.153 |
r_mcbond_it | 2.417 |
r_mcbond_other | 2.346 |
r_angle_refined_deg | 1.623 |
r_angle_other_deg | 0.999 |
r_chiral_restr | 0.095 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1871 |
Nucleic Acid Atoms | |
Solvent Atoms | 182 |
Heterogen Atoms | 57 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |