5IG6
Ultra-high resolution crystal structure of second bromodomain of BRD2 in complex with inhibitor 6B3
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2E3K |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 300 | 30% PEG MME 2000, 50mM Tris-HCl pH 7.5, 50mM NaCl, 20% glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.62 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 32 | ¦Á = 90 |
b = 52.37 | ¦Â = 90 |
c = 71.46 | ¦Ã = 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 | CCD | MARMOSAIC 225 mm CCD | 2015-07-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.7293 | ESRF | BM14 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | CC (Half) | 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 | 0.91 | 42.22 | 99.4 | 0.054 | 0.054 | 0.999 | 11.6 | 4.4 | 86054 | 7.031 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 0.91 | 0.96 | 100 | 1.627 | 0.9 | 4.1 |
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 | 2E3k | 0.91 | 20 | 81790 | 4328 | 99.16 | 0.1262 | 0.12526 | 0.14336 | RANDOM | 12.231 |
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] | |
0.17 | 0.06 | -0.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.68 |
r_sphericity_free | 26.73 |
r_dihedral_angle_4_deg | 21.56 |
r_dihedral_angle_3_deg | 12.673 |
r_sphericity_bonded | 7.999 |
r_dihedral_angle_1_deg | 4.866 |
r_rigid_bond_restr | 3.674 |
r_angle_refined_deg | 1.812 |
r_angle_other_deg | 0.947 |
r_chiral_restr | 0.11 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 945 |
Nucleic Acid Atoms | |
Solvent Atoms | 213 |
Heterogen Atoms | 47 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALA | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |