3Q4T
Crystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with dorsomorphin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2QLU | pdb id 2qlu |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.8 | 293.15 | 28% PEG 3350, 0.2M LiSO4, 0.1M Tris, pH 8.8, 10% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.48 | 50.33 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 110.1 | α = 90 |
b = 110.1 | β = 90 |
c = 206.911 | γ = 120 |
Symmetry | |
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Space Group | P 65 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 Q315 3x3 CCD | Kirkpatrick Baez bimorph mirror pair | 2010-04-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9763 | Diamond | I03 |
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 | 1.96 | 48.6 | 99.9 | 0.112 | 11.2 | 7 | 53883 | 53760 | 26.6 |
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 | 1.96 | 2.07 | 100 | 0.783 | 2.3 | 7.2 | 7727 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Number Reflections (All) | 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 id 2qlu | 1.96 | 45.47 | 2 | 53760 | 51027 | 2733 | 99.8 | 0.17124 | 0.16847 | 0.22301 | RANDOM | 24.429 |
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] | |
0.83 | 0.42 | 0.83 | -1.25 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.943 |
r_dihedral_angle_4_deg | 17.193 |
r_dihedral_angle_3_deg | 13.573 |
r_scangle_it | 9.781 |
r_scbond_it | 7.176 |
r_dihedral_angle_1_deg | 6.32 |
r_mcangle_it | 4.46 |
r_mcbond_it | 2.974 |
r_angle_refined_deg | 1.561 |
r_angle_other_deg | 0.975 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4857 |
Nucleic Acid Atoms | |
Solvent Atoms | 496 |
Heterogen Atoms | 177 |
Software
Software | |
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Software Name | Purpose |
GDA | data collection |
PHASER | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |