5FE1
Crystal structure of human PCAF bromodomain in complex with fragment BR004 (fragment 1)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3GG3 | pdb id 3GG3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277.15 | 21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.52 | 65.09 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 99.67 | α = 90 |
b = 99.67 | β = 90 |
c = 100.4 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
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 | 2011-09-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E SUPERBRIGHT | 1.54178 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.22 | 33.47 | 100 | 0.092 | 11.2 | 4.4 | 18352 | 43.5 |
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 | 2.22 | 2.34 | 100 | 0.728 | 2 | 4.3 |
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 | pdb id 3GG3 | 2.22 | 33.47 | 17400 | 940 | 99.91 | 0.20991 | 0.20831 | 0.24083 | RANDOM | 44.942 |
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] | |
-0.1 | -0.05 | -0.1 | 0.31 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.941 |
r_dihedral_angle_4_deg | 19.2 |
r_dihedral_angle_3_deg | 13.899 |
r_dihedral_angle_1_deg | 5.89 |
r_long_range_B_refined | 5.387 |
r_long_range_B_other | 5.387 |
r_scangle_other | 2.774 |
r_mcangle_it | 2.14 |
r_mcangle_other | 2.139 |
r_scbond_it | 1.647 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1780 |
Nucleic Acid Atoms | |
Solvent Atoms | 153 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |