2G8T
Indole-amidine Complexes with Bovine Trypsin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | Trypsin, final concentration of 0.6 mM, was dissolved in 20 mM HEPES pH 7.0, 10 mM calcium chloride, 3% DMSO, and 3 mM of ligand of interest (compounds 3, 6, and 9). The well solution consisted of 100 mM Cacodylate pH 6.5, 200 mM ammonium sulfate, 50% PEG (17% to 28%). The ligands were co crystallized with protein using vapor diffusion and hanging drop method. The drops were 1:1 (protein:well solution) and the plates were stored at 20 degrees centigrade. The crystals were generally present within two days. The cryo-protectant consisted of adding 75 l of an adjusted well solution, adjusted with PEG 8000 to 0.5% higher, and 25 l of glycerol. drop 1:1, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.98 | 37.96 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.525 | α = 90 |
b = 54.525 | β = 90 |
c = 107.807 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | ADSC QUANTUM 4 | Mirrors | 2005-12-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1 | APS | 17-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.41 | 43.25 | 99.8 | 36557 | 36505 | 3 | 4 | 13.9 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1.41 | 1.5 | 99.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.41 | 43.25 | 36557 | 36505 | 3644 | 99.8 | 0.191 | 0.191 | 0.19 | 0.2 | RANDOM | 15.5 |
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] | |
-0.03 | -0.28 | -0.03 | 0.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 25.3 |
c_scangle_it | 2.56 |
c_scbond_it | 2 |
c_angle_deg | 1.4 |
c_mcangle_it | 1.38 |
c_mcbond_it | 0.9 |
c_improper_angle_d | 0.76 |
c_bond_d | 0.006 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1632 |
Nucleic Acid Atoms | |
Solvent Atoms | 298 |
Heterogen Atoms | 25 |
Software
Software | |
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Software Name | Purpose |
CNX | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |