7A0F
The Crystal Structure of Bovine Thrombin in complex with Hirudin (C22U/C39U) at 2.7 Angstroms Resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.7 | 297 | 38% PEG 4000, 0.1 M sodium phosphate (pH= 4.7), 0.3 M NaCl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.46 | 49.97 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.069 | α = 90 |
b = 101.498 | β = 90 |
c = 142.075 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | 2019-12-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, DESY BEAMLINE P11 | 0.9778 | PETRA III, DESY | P11 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.7 | 47.79 | 100 | 0.287 | 0.287 | 0.299 | 0.082 | 0.992 | 8.9 | 13.1 | 11928 |
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) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 2.7 | 2.83 | 1.8 | 1.8 | 1.873 | 0.514 | 0.592 | 1.6 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7A0D | 2.7 | 47.79 | 11902 | 586 | 99.933 | 0.196 | 0.1936 | 0.2532 | 45.168 |
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] | |
-0.848 | 0.639 | 0.209 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.42 |
r_dihedral_angle_4_deg | 20.966 |
r_dihedral_angle_3_deg | 17.975 |
r_lrange_it | 10.929 |
r_dihedral_angle_1_deg | 10.113 |
r_scangle_it | 6.841 |
r_mcangle_it | 5.638 |
r_scbond_it | 4.378 |
r_mcbond_it | 3.456 |
r_angle_refined_deg | 1.744 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2848 |
Nucleic Acid Atoms | |
Solvent Atoms | 73 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
XDS | data processing |
Aimless | data reduction |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |
REFMAC | refinement |