5TPX
Bromodomain from Plasmodium Faciparum Gcn5, complexed with compound
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | The protein was crystallized at 293 K in 0.1M CaCl2, 30% PEG 8K, 0.2M NH4SO4 with 2mM compound using the sitting drop method. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.36 | 47.94 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 75 | α = 90 |
b = 75 | β = 90 |
c = 49.62 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 4 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | 2016-09-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | 0.98011 | CLSI | 08ID-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.1 | 37.55 | 96 | 0.1 | 6.8 | 7.8 | 8411 | 38.07 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.1 | 2.14 | 89 | 0.725 | 0.877 | 7.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 4QNS | 2.1 | 37.5 | 8368 | 390 | 96.1 | 0.188 | 0.185 | 0.236 | RANDOM | 45.42 |
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] | |
6.2745 | 6.2745 | -12.5489 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_other_torsion | 14.05 |
t_omega_torsion | 3.7 |
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 | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 870 |
Nucleic Acid Atoms | |
Solvent Atoms | 66 |
Heterogen Atoms | 43 |
Software
Software | |
---|---|
Software Name | Purpose |
HKL-2000 | data collection |
HKL-2000 | data scaling |
BUSTER-TNT | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |
DENZO | data reduction |
SCALEPACK | data scaling |
BUSTER | refinement |