3U5P
Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | 0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.33 | 47.15 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 63.426 | α = 90.01 |
b = 63.608 | β = 90.04 |
c = 124.611 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 197 | CCD | ADSC QUANTUM 315 | 2011-05-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X25 | 1.10000 | NSLS | X25 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.8 | 30 | 98.6 | 0.047 | 26.6 | 3.4 | 47438 | -3 | -3 | 52.6 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.8 | 2.9 | 98 | 0.41 | 2.1 | 3.5 | 4785 |
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 | 3U5M | 2.8 | 30 | 43152 | 2264 | 93.97 | 0.21317 | 0.21048 | 0.26478 | RANDOM | 94.357 |
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] | |
-0.6 | -0.14 | 0.18 | -0.5 | -0.05 | 1.1 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.377 |
r_dihedral_angle_3_deg | 22.085 |
r_dihedral_angle_4_deg | 17.278 |
r_dihedral_angle_1_deg | 5.837 |
r_angle_refined_deg | 1.557 |
r_chiral_restr | 0.098 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 13245 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 16 |
Software
Software | |
---|---|
Software Name | Purpose |
CBASS | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |