4QYL
Crystal Structure of the human BRPF1 bromodomain in complex with a histone H2AK5ac peptide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3RCW | PDB entry 3RCW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 0.2 M NH4SO4, 0.1 M MES monohydrate, pH 6.5, 30% w/v polyethylene glycol monomethyl ether (PEG) 5000, 1% propylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 47.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.908 | α = 90 |
b = 55.581 | β = 93.58 |
c = 82.135 | 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 | CCD | ADSC QUANTUM 315r | 2013-04-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 1.075 | NSLS | X29A |
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 | 1.8 | 41.02 | 99.9 | 0.081 | 21.04 | 4 | 48421 | 48421 | 3 |
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 | 1.8 | 1.83 | 100 | 0.386 | 3 | 3.9 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 3RCW | 1.8 | 41.02 | 48421 | 48421 | 2587 | 99.97 | 0.20629 | 0.20389 | 0.25257 | RANDOM | 20.965 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.35 | -0.09 | 0.66 | -1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.971 |
r_dihedral_angle_3_deg | 12.263 |
r_dihedral_angle_4_deg | 8.287 |
r_dihedral_angle_1_deg | 5.89 |
r_angle_refined_deg | 1.775 |
r_angle_other_deg | 1.351 |
r_chiral_restr | 0.112 |
r_bond_refined_d | 0.019 |
r_gen_planes_refined | 0.012 |
r_bond_other_d | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4087 |
Nucleic Acid Atoms | |
Solvent Atoms | 722 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |