3UP7
Aurora A in complex with YL1-038-09
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3FDN | PDB ENTRY 3FDN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 10 mg/mL AURORA A protein, 1 mM YL1-038-09, 10 % (v/v) PEG 3350, 25 mM phosphate(Na/K pH 7.4), 100 mM sodium tartrate pH 7.0 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.62 | 53.08 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 82.58 | α = 90 |
b = 82.58 | β = 90 |
c = 172.36 | γ = 120 |
Symmetry | |
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Space Group | P 61 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 | 93 | CCD | RIGAKU SATURN 944+ | MIRRORS | 2010-06-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54178 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 3.05 | 20 | 99.3 | 0.068 | 0.05 | 31.67 | 4.9 | 7101 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.05 | 3.1 | 100 | 0.371 | 0.345 | 4.7 | 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 | PDB ENTRY 3FDN | 3.05 | 19.61 | 7101 | 320 | 99.8 | 0.233 | 0.233 | 0.292 | RANDOM | 56.6 |
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] | |
-1.68 | -1.68 | 3.36 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.8 |
c_scangle_it | 2.41 |
c_mcangle_it | 2.11 |
c_angle_deg | 1.7 |
c_scbond_it | 1.51 |
c_mcbond_it | 1.14 |
c_improper_angle_d | 1.05 |
c_bond_d | 0.011 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2172 |
Nucleic Acid Atoms | |
Solvent Atoms | 14 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
StructureStudio | data collection |
PHENIX | model building |
CNS | refinement |
XDS | data reduction |
XDS | data scaling |
PHENIX | phasing |