Crystal structure of Human Fibroblast Growth Factor Receptor 1 Kinase domain in complex with compound 1
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1FGK | PDB ENTRY 1FGK |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 277 | 16-20% PEG8000, 100 mM PCTP, 100-300 mM ammonium sulfate, 25% ethylene glycol, pH 6.25-7.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.66 | 53.76 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 208.306 | α = 90 |
| b = 57.477 | β = 107.42 |
| c = 65.452 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 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 | 110 | CCD | RIGAKU SATURN 92 | 2004-12-22 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.54179 | ||
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 | 2.55 | 17.33 | 97.03 | 0.093 | 8.76 | 2.63 | 24314 | 23652 | 1 | 1 | |||||||||
| 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 | 2.55 | 2.69 | 97.84 | 0.71 | 1.82 | 2.59 | |||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1FGK | 2.55 | 17.33 | 22438 | 1214 | 97.28 | 0.23223 | 0.2293 | 0.24 | 0.28741 | 0.28 | RANDOM | 35.576 | ||||
| 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] | |
| -1.71 | -0.98 | 3.56 | -2.43 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.489 |
| r_dihedral_angle_4_deg | 15.581 |
| r_dihedral_angle_3_deg | 14.958 |
| r_dihedral_angle_1_deg | 6.13 |
| r_scangle_it | 2.744 |
| r_scbond_it | 2.39 |
| r_angle_refined_deg | 1.421 |
| r_mcangle_it | 0.964 |
| r_angle_other_deg | 0.812 |
| r_mcbond_it | 0.767 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4229 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 28 |
| Heterogen Atoms | 62 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CrystalClear | data collection |
| AMoRE | phasing |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
