5OXG
Crystal structure of the ACVR1 (ALK2) kinase in complex with LDN-212854
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3H9R |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 277 | 18% PEG8000 -- 0.2M calcium acetate -- 0.1M cacodylate pH 6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.81 | 56.29 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 85.86 | α = 90 |
b = 102.201 | β = 93.96 |
c = 177.3 | γ = 90 |
Symmetry | |
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Space Group | I 1 2 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 | PIXEL | DECTRIS PILATUS 6M | Kirkpatrick Baez bimorph mirror pair for horizontal and vertical focusing | 2013-12-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9762 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.13 | 65.65 | 99.56 | 0.077 | 0.093 | 0.052 | 0.991 | 8 | 3.1 | 88737 | 2 | 40.8 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.1 | 2.14 | 99.6 | 0.539 | 0.65 | 0.358 | 0.8 | 1.9 | 3.1 |
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 | 3H9R | 2.13 | 65.65 | 84441 | 4290 | 99.58 | 0.20736 | 0.20611 | 0.23243 | RANDOM | 45.974 |
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] | |
-2.4 | 2.81 | 1 | 1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.363 |
r_dihedral_angle_4_deg | 21.385 |
r_dihedral_angle_3_deg | 13.648 |
r_long_range_B_other | 11.352 |
r_long_range_B_refined | 11.351 |
r_dihedral_angle_1_deg | 6.088 |
r_scangle_other | 4.533 |
r_mcangle_it | 4.174 |
r_mcangle_other | 4.173 |
r_scbond_it | 2.932 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9312 |
Nucleic Acid Atoms | |
Solvent Atoms | 353 |
Heterogen Atoms | 134 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |