6LVL
Crystal structure of FGFR2 in complex with 1,3,5-triazine derivative
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3B2T |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 296 | Tris, Ammonium sulfate, PEG 8000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.75 | 55.28 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 105.675 | α = 90 |
b = 116.136 | β = 90 |
c = 64.202 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 90 | CCD | ADSC QUANTUM 270 | 2009-12-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NE3A | 1 | Photon Factory | AR-NE3A |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.98 | 50 | 87.7 | 0.119 | 9.9 | 3.9 | 14661 |
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 | 2.99 | 3.04 | 91.3 | 0.357 | 3.9 |
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 | 3B2T | 2.98 | 28.11 | 13920 | 721 | 87.49 | 0.2043 | 0.2019 | 0.2506 | RANDOM | 26.484 |
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] | |
-1.18 | -0.03 | 1.21 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.485 |
r_dihedral_angle_3_deg | 19.025 |
r_dihedral_angle_4_deg | 17.491 |
r_dihedral_angle_1_deg | 7.358 |
r_angle_refined_deg | 1.658 |
r_chiral_restr | 0.127 |
r_bond_refined_d | 0.005 |
r_gen_planes_refined | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4576 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 102 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
PHASER | phasing |