5G15
Structure Aurora A (122-403) bound to activating monobody Mb1 and AMPPCP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 291 | AURORA A AND MONOBODIES WERE ALIQUOTED IN STORAGE BUFFER (20MM TRISHCL, 200MM NACL, 10% (V/V) GLYCEROL, 20MM MGCL2, 5MM TCEP, PH 7.50) AND KEPT AT -80C. AMPPCP WAS PREPARED FRESH FROM POWDER THE DAY OF CRYSTALLIZATION IN CONCENTRATIONS OF 100-120MM IN STORAGE BUFFER. CRYSTALS OF AURA IN COMPLEX WITH AMPPCP AND ACTIVATING MONOBODY, MB1, WERE OBTAINED BY COMBINING 0.5UL OF [300UM AURA WITH 5MM AMPPCP AND 300UM MB1] WITH 0.5UL OF MOTHER LIQUOR (0.1M MES SODIUM SALT PH 6.50, 0.2M AMMONIUM SULFATE, 4% (V/V) 1,3-PROPANEDIOL, 30% (W/V) PEG8000). CRYSTALS WERE GROWN AT 18C BY VAPOR DIFFUSION AND THE SITTING DROP METHOD. THE CRYSTALS WERE WASHED WITH MOTHER LIQUOR AND FLASH FROZEN IN LIQUID NITROGEN IN PREPARATION FOR DATA COLLECTION. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.86 | 57.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 75.339 | α = 90 |
b = 91.361 | β = 90 |
c = 143.715 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 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 | CCD | ADSC QUANTUM 315 | 2015-05-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | ALS | 8.2.2 |
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 | 2.06 | 58.13 | 100 | 0.13 | 10.3 | 7.2 | 30879 | 1.8 |
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 | 2.06 | 2.12 | 99.5 | 1.21 | 1.8 | 7.2 |
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 ENTRIES 4C3R AND 3K2M | 2.06 | 77.1 | 29755 | 1052 | 99.71 | 0.22853 | 0.22687 | 0.27388 | RANDOM | 34.133 |
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] | |
-0.02 | 0.01 | 0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.402 |
r_dihedral_angle_3_deg | 16.379 |
r_dihedral_angle_4_deg | 14.611 |
r_dihedral_angle_1_deg | 7.235 |
r_mcangle_it | 4.45 |
r_scbond_it | 3.536 |
r_mcbond_it | 2.914 |
r_mcbond_other | 2.895 |
r_angle_refined_deg | 1.916 |
r_angle_other_deg | 1.046 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2873 |
Nucleic Acid Atoms | |
Solvent Atoms | 145 |
Heterogen Atoms | 52 |
Software
Software | |
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Software Name | Purpose |
DIALS | data reduction |
Aimless | data scaling |
MOLREP | phasing |
PHASER | phasing |
REFMAC | refinement |