5DNR
Aurora A Kinase in complex with ATP in space group P41212
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3FDN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 292 | 100 mM HEPES, 200 mM magnesium sulfate, 2-20% PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.61 | 65.96 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.46 | α = 90 |
b = 81.46 | β = 90 |
c = 137.38 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | PIXEL | DECTRIS PILATUS 6M-F | 2014-07-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.92 | Diamond | I04-1 |
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 | 1.95 | 57.6 | 99.9 | 0.054 | 27.7 | 12.9 | 34608 | 35.38 |
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 | 1.95 | 2 | 99.8 | 0.67 | 4.2 | 13.5 |
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 | 3FDN | 1.95 | 18.22 | 32728 | 1652 | 99.74 | 0.20642 | 0.2055 | 0.22552 | RANDOM | 40.296 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.767 |
r_dihedral_angle_4_deg | 17.429 |
r_dihedral_angle_3_deg | 14.491 |
r_long_range_B_other | 11.108 |
r_long_range_B_refined | 11.084 |
r_scangle_other | 9.805 |
r_scbond_it | 7.344 |
r_scbond_other | 7.341 |
r_mcangle_other | 4.063 |
r_mcangle_it | 3.942 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2173 |
Nucleic Acid Atoms | |
Solvent Atoms | 120 |
Heterogen Atoms | 38 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
PHASER | phasing |
XSCALE | data scaling |