5D7V
Crystal structure of PTK6 kinase domain
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2F4J |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 298 | 0.23M Diammonium Phosphate, 18% PEG 3350, 1M Lithium chloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.48 | 50.39 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.718 | α = 81.46 |
b = 76.308 | β = 75.92 |
c = 87.271 | γ = 74.93 |
Symmetry | |
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Space Group | P 1 |
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 | 100 | IMAGE PLATE | MAR scanner 345 mm plate | VariMax HR | 2015-03-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54789 |
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 | 2.33 | 50 | 96.3 | 0.113 | 7.3 | 2.1 | 50742 |
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 | 2.33 | 2.41 | 94.2 | 0.443 | 1.9 | 2.1 |
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 | 2F4J | 2.33 | 50 | 46364 | 2476 | 95.98 | 0.2218 | 0.2186 | 0.2816 | RANDOM | 26.633 |
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] | |
1.67 | -0.49 | 0.87 | -0.61 | -0.29 | -1.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.401 |
r_dihedral_angle_3_deg | 17.169 |
r_dihedral_angle_4_deg | 16.644 |
r_dihedral_angle_1_deg | 5.813 |
r_scangle_it | 1.491 |
r_angle_refined_deg | 1.175 |
r_scbond_it | 0.922 |
r_mcangle_it | 0.689 |
r_mcbond_it | 0.387 |
r_nbtor_refined | 0.295 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8592 |
Nucleic Acid Atoms | |
Solvent Atoms | 366 |
Heterogen Atoms | 92 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |