3BKB
Crystal structure of human Feline Sarcoma Viral Oncogene Homologue (v-FES)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2HYY | An ensemble of three kinase domains from the PDB entries 2HYY, 2G2I, 2G2H |
experimental model | PDB | 2G2I | An ensemble of three kinase domains from the PDB entries 2HYY, 2G2I, 2G2H |
experimental model | PDB | 2G2H | An ensemble of three kinase domains from the PDB entries 2HYY, 2G2I, 2G2H |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | 0.2M Na2SO4, 0.1M Bis-Tris-Propane, 20% PEG 3350, 10% Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.87 | 57.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.404 | α = 90 |
b = 80.404 | β = 90 |
c = 131.411 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 225 mm CCD | 2007-08-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 0.98074 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.78 | 43.81 | 100 | 0.128 | 0.128 | 18.7 | 14.1 | 46019 | 46019 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.78 | 1.88 | 100 | 0.787 | 0.787 | 2 | 5.9 | 6704 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | An ensemble of three kinase domains from the PDB entries 2HYY, 2G2I, 2G2H | 1.78 | 43.81 | 45977 | 45977 | 2312 | 99.93 | 0.15 | 0.15 | 0.148 | 0.189 | RANDOM | 21.662 |
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] | |
0.39 | 0.19 | 0.39 | -0.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.042 |
r_dihedral_angle_4_deg | 12.284 |
r_dihedral_angle_3_deg | 12.098 |
r_dihedral_angle_1_deg | 5.941 |
r_mcbond_it | 3.545 |
r_angle_refined_deg | 1.532 |
r_angle_other_deg | 1.118 |
r_mcbond_other | 0.942 |
r_symmetry_vdw_other | 0.265 |
r_nbd_refined | 0.204 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2927 |
Nucleic Acid Atoms | |
Solvent Atoms | 388 |
Heterogen Atoms | 82 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrystalClear | data collection |
MOSFLM | data reduction |