3TLP
Crystal structure of the fourth 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 | 3HMF | PDB entries 3HMF, 2OO1, 3DAI, 3HMH, 2OSS, 2OUO, 3D7C, 3DWY |
experimental model | PDB | 2OO1 | PDB entries 3HMF, 2OO1, 3DAI, 3HMH, 2OSS, 2OUO, 3D7C, 3DWY |
experimental model | PDB | 3DAI | PDB entries 3HMF, 2OO1, 3DAI, 3HMH, 2OSS, 2OUO, 3D7C, 3DWY |
experimental model | PDB | 3HMH | PDB entries 3HMF, 2OO1, 3DAI, 3HMH, 2OSS, 2OUO, 3D7C, 3DWY |
experimental model | PDB | 2OSS | PDB entries 3HMF, 2OO1, 3DAI, 3HMH, 2OSS, 2OUO, 3D7C, 3DWY |
experimental model | PDB | 2OUO | PDB entries 3HMF, 2OO1, 3DAI, 3HMH, 2OSS, 2OUO, 3D7C, 3DWY |
experimental model | PDB | 3D7C | PDB entries 3HMF, 2OO1, 3DAI, 3HMH, 2OSS, 2OUO, 3D7C, 3DWY |
experimental model | PDB | 3DWY | PDB entries 3HMF, 2OO1, 3DAI, 3HMH, 2OSS, 2OUO, 3D7C, 3DWY |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 277 | 25% PEG_MME_2000, 0.015M NiCl, 0.1M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.34 | 47.47 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.431 | α = 90 |
b = 60.22 | β = 90 |
c = 109.907 | 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 | PIXEL | PSI PILATUS 6M | 2011-07-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 1.000 | Diamond | I03 |
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 | 2.13 | 19.75 | 99.4 | 0.062 | 0.062 | 14.3 | 4.4 | 18984 | 18871 | 44.7 |
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 | 2.13 | 2.25 | 99.8 | 0.88 | 0.88 | 0.9 | 4.3 | 2738 |
Refinement
Statistics | |||||||||||||||||||
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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 3HMF, 2OO1, 3DAI, 3HMH, 2OSS, 2OUO, 3D7C, 3DWY | 2.13 | 19.75 | 19003 | 18831 | 973 | 99.09 | 0.2037 | 0.2037 | 0.2014 | 0.2486 | RANDOM | 50.8461 |
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] | |
0.51 | 0.04 | -0.54 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.493 |
r_dihedral_angle_4_deg | 20.708 |
r_dihedral_angle_3_deg | 15.792 |
r_dihedral_angle_1_deg | 5.315 |
r_angle_refined_deg | 1.324 |
r_angle_other_deg | 1.173 |
r_chiral_restr | 0.08 |
r_bond_refined_d | 0.016 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1889 |
Nucleic Acid Atoms | |
Solvent Atoms | 78 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
GDA | data collection |
XDS | data reduction |