5L6O
EphB3 kinase domain covalently bound to an irreversible inhibitor (compound 3)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | 1,4-dioxane, Tris buffer, magnesium chloride |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.26 | 45.58 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 46.817 | α = 90 |
b = 57.214 | β = 90 |
c = 113.184 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2016-01-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | 0.97949 | Diamond | I02 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 1.88 | 57.21 | 100 | 0.049 | 0.999 | 17.6 | 6.2 | 25671 | 37.27 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.88 | 1.98 | 100 | 0.548 | 2.5 | 4.8 |
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 | 3ZFY | 1.88 | 56.59 | 25443 | 1219 | 100 | 0.19 | 0.189 | 0.206 | RANDOM | 68.56 |
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] | |
3.2447 | 6.6717 | -9.9164 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_other_torsion | 16.51 |
t_omega_torsion | 2.79 |
t_angle_deg | 0.93 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2071 |
Nucleic Acid Atoms | |
Solvent Atoms | 94 |
Heterogen Atoms | 26 |
Software
Software | |
---|---|
Software Name | Purpose |
BUSTER | refinement |
Aimless | data scaling |
MOLREP | phasing |
PDB_EXTRACT | data extraction |
XDS | data reduction |
XDS | data scaling |