6ZV8
Crystal Structure of Thrombin in complex with compound51
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 283 | 0.02 M phosphate buffer pH 7.5, 27% PEG 8000, 100 mM NaCl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.42 | 49.17 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 69.166 | α = 90 |
b = 70.342 | β = 100.28 |
c = 71.372 | γ = 90 |
Symmetry | |
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Space Group | C 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 | CCD | Nonius Kappa CCD | MIRRORS | 2012-11-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.54187 |
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 | 1.59 | 70.23 | 89.2 | 0.06 | 12.95 | 2.84 | 130734 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.59 | 1.61 | 89 | 0.279 | 1.96 |
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 | INHOUSE | 1.7 | 70.22 | 31333 | 1618 | 88.88 | 0.2052 | 0.203 | 0.2473 | RANDOM | 18.885 |
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] | |
0.57 | -0.38 | -0.45 | -0.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
TORSION ANGLES, PERIOD 2 (DEGREES) | 33.059 |
TORSION ANGLES, PERIOD 3 (DEGREES) | 14.353 |
TORSION ANGLES, PERIOD 4 (DEGREES) | 12.948 |
TORSION ANGLES, PERIOD 1 (DEGREES) | 6.86 |
BOND ANGLES REFINED (DEGREES) | 2.212 |
BOND ANGLES OTHERS (DEGREES) | 0.915 |
CHIRAL-CENTER RESTRAINTS (A**3) | 0.121 |
BOND LENGTHS REFINED (A) | 0.023 |
GENERAL PLANES REFINED (A) | 0.012 |
BOND LENGTHS OTHERS (A) | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2342 |
Nucleic Acid Atoms | |
Solvent Atoms | 258 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
SAINT | data reduction |
XPREP | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |