4UXL
Structure of Human ROS1 Kinase Domain in Complex with PF-06463922
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3ZBF | PDB ENTRY 3ZBF |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 286 | CRYSTALS WERE OBTAINED BY THE HANGING DROP VAPOR DIFFUSION METHOD AT 13 DEGREES C BY MIXING 1.5 MICROLITERS OF SOLUTION CONTAINING A 1:3 MOLAR RATIO OF PHOSPHORYLATED ROS1 KD (12.2MG/ML) TO PF-06463922 AND 1.5 MICROLITERS OF RESERVOIR SOLUTION CONTAINING 25% (W/V) PEG 3350, 0.6M POTASSIUM THIOCYANATE AND 0.1M SODIUM CITRATE TRIBASIC DIHYDRATE, PH5.6. CRYSTALS WERE FLASH-FROZEN IN LIQUID NITROGEN AFTER TRANSFER TO 2 MICROLITERS OF RESERVOIR SOLUTION CONTAINING 25% (V/V) GLYCEROL AS A CRYOPROTECTANT. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 55 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 105.844 | ¦Á = 90 |
b = 105.844 | ¦Â = 90 |
c = 49.843 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 64 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 87 | PIXEL | DECTRIS PILATUS 6M | 2012-04-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | APS | 17-ID |
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 | 2.21 | 91.66 | 97.1 | 0.04 | 27 | 6.7 | 15684 | 2 | 41.4 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.21 | 2.33 | 62.1 | 0.42 | 2.8 | 4.4 |
Refinement
Statistics | |||||||||||||||||||
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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 | PDB ENTRY 3ZBF | 2.4 | 91.66 | 12648 | 379 | 100 | 0.211 | 0.211 | 0.281 | RANDOM | 50.4 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-5.98 | 2.43 | -5.98 | 11.97 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.8 |
c_scangle_it | 3.11 |
c_mcangle_it | 2.82 |
c_scbond_it | 2.13 |
c_mcbond_it | 1.66 |
c_angle_deg | 0.9 |
c_improper_angle_d | 0.62 |
c_bond_d | 0.006 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2310 |
Nucleic Acid Atoms | |
Solvent Atoms | 136 |
Heterogen Atoms | 30 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
autoPROC | data reduction |
SCALA | data scaling |
CNX | phasing |