5VS7
Bromodomain of PF3D7_1475600 from Plasmodium falciparum complexed with peptide H4K5ac
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.9 | 277 | The protein was crystallized at 277K in 25% PEG3350, 0.1 M HEPES pH 7.9, using the vapor diffusion sitting drop method. Final concentration of 2 mM peptide H4K5ac (GRGKacGGK) was added directly to the concentrated protein immediately prior to setting up the crystallization plate. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.01 | 38.81 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.11 | α = 90 |
b = 41.51 | β = 90 |
c = 73.09 | 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 | DECTRIS PILATUS3 S 6M | 2017-02-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97914 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.04 | 40 | 99.5 | 0.074 | 0.08 | 0.031 | 7.2 | 6.5 | 8199 | 46.73 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.04 | 2.08 | 99 | 0.573 | 0.071 | 0.028 | 0.997 | 5.1 |
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 | 4NXJ | 2.04 | 36.54 | 8143 | 389 | 99.2 | 0.212 | 0.21 | 0.244 | RANDOM | 58.82 |
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] | |
6.2593 | -1.8272 | -4.432 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 15.68 |
t_omega_torsion | 3.54 |
t_angle_deg | 0.67 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1032 |
Nucleic Acid Atoms | |
Solvent Atoms | 60 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
HKL-2000 | data collection |
HKL-2000 | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |
DENZO | data reduction |
SCALEPACK | data scaling |