3UV2
Crystal structure of the bromodomain of human nucleosome-remodeling factor subunit BPTF
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2NXB | Ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI |
experimental model | PDB | 2OO1 | Ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI |
experimental model | PDB | 2OSS | Ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI |
experimental model | PDB | 2OUO | Ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI |
experimental model | PDB | 2RFJ | Ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI |
experimental model | PDB | 3DAI | Ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 0.10M Na/KPO4, 20.0% PEG 3350, 10.0% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 46.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 27.141 | α = 90 |
b = 66.809 | β = 106.16 |
c = 39.259 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | 2008-07-03 | 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 | 1.58 | 25 | 93.3 | 0.05 | 0.05 | 15.9 | 3.7 | 18460 | 17223 | 19.6 |
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 | 1.58 | 1.67 | 79.5 | 0.518 | 0.518 | 1.5 | 3.4 | 2102 |
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 | Ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI | 1.58 | 25 | 18457 | 17222 | 881 | 93.31 | 0.1647 | 0.1647 | 0.1623 | 0.209 | RANDOM | 18.3808 |
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] | |
0.23 | 0.59 | -0.51 | 0.61 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.25 |
r_dihedral_angle_4_deg | 17.842 |
r_dihedral_angle_3_deg | 12.553 |
r_dihedral_angle_1_deg | 4.967 |
r_angle_refined_deg | 1.671 |
r_angle_other_deg | 0.957 |
r_chiral_restr | 0.098 |
r_bond_refined_d | 0.016 |
r_gen_planes_refined | 0.009 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 983 |
Nucleic Acid Atoms | |
Solvent Atoms | 204 |
Heterogen Atoms | 10 |
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 |