6HH1
Structure of c-Kit with allosteric inhibitor 3G8
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.4 | 293 | 9.3 mg/mL protein in 250 mM NaCl, 25 mM Tris-HCl pH 7.4, 1 mM EDTA, 0.5 mM TCEP, 1.2 mM 3G8, 0.1% w/w V8 protease. 800 nL of protein was mixed with 800 nL of crystallization solution (0.1 M Tris-HCl pH 9.1, 1.5 M diammonium hydrogen phosphate) and incubated over 0.4 mL crystallization solution in 24 well VDX plates. Crystals were cryo-protected with 20% v/v ethylene glycol. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.38 | 48.32 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 65.614 | α = 90 |
b = 65.614 | β = 90 |
c = 159.004 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 32 2 1 |
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 | ADSC QUANTUM 315r | 2012-09-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.976 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim 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 | 2.15 | 20 | 97.65 | 0.13 | 5.42 | 3.94 | 21244 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.15 | 2.27 | 99.81 | 0.8 | 1.6 | 4.05 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | FOURIER SYNTHESIS | THROUGHOUT | 2.25 | 25.32 | 17585 | 940 | 94.72 | 0.208 | 0.2045 | 0.2734 | RANDOM | 62.078 |
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] | |
-0.94 | -0.47 | -0.94 | 3.05 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.871 |
r_dihedral_angle_4_deg | 23.022 |
r_dihedral_angle_3_deg | 18.937 |
r_dihedral_angle_1_deg | 6.868 |
r_angle_refined_deg | 1.896 |
r_angle_other_deg | 1.321 |
r_chiral_restr | 0.087 |
r_bond_refined_d | 0.011 |
r_gen_planes_refined | 0.009 |
r_gen_planes_other | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2400 |
Nucleic Acid Atoms | |
Solvent Atoms | 122 |
Heterogen Atoms | 32 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
SCALA | data scaling |