7A0E
The Crystal Structure of Bovine Thrombin in complex with Hirudin (C6U/C14U) at 1.9 Angstroms Resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7A0D |
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), and 0.2 M NaCl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 52.62 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.099 | α = 90 |
b = 101.995 | β = 90 |
c = 144.044 | 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 EIGER2 XE 16M | 2020-02-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9763 | Diamond | I04 |
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 | 1.9 | 72.02 | 98.05 | 0.206 | 0.206 | 0.216 | 0.062 | 0.992 | 5 | 10.6 | 33481 |
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 | 1.9 | 1.93 | 1.848 | 1.848 | 2.148 | 1.061 | 0.873 | 0.2 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7A0D | 1.9 | 72.02 | 33424 | 1572 | 97.894 | 0.216 | 0.2139 | 0.2629 | 40.955 |
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] | |
0.548 | -0.38 | -0.168 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.672 |
r_dihedral_angle_4_deg | 19.236 |
r_dihedral_angle_3_deg | 16.33 |
r_lrange_it | 8.384 |
r_dihedral_angle_1_deg | 7.362 |
r_scangle_it | 5.734 |
r_mcangle_it | 4.208 |
r_scbond_it | 3.906 |
r_mcbond_it | 2.78 |
r_angle_refined_deg | 1.453 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2852 |
Nucleic Acid Atoms | |
Solvent Atoms | 215 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
xia2 | data processing |
xia2 | data reduction |
xia2 | data scaling |
PHASER | phasing |
Coot | model building |
REFMAC | refinement |