3T26
Orthorhombic trypsin (bovine) in the presence of sarcosine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1TPO | PDB entry 1TPO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 298 | 40 mg/mL protein in water, 25% (w/v) P8K, 0.2 M AmSO4, 0.1 M benzamidine, 0.1 M Tris, pH 8.0, Soaked in 4 M sarcosine, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.34 | 47.34 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 54.923 | ¦Á = 90 |
b = 58.553 | ¦Â = 90 |
c = 67.764 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 298 | CCD | OXFORD ONYX CCD | 2011-06-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | OTHER | 1.54 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.7 | 44.3 | 99.9 | 0.087 | 11.8 | 5.6 | 24708 | 24708 |
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) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.7 | 1.79 | 99.9 | 0.522 | 0.522 | 1.3 | 4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | PDB entry 1TPO | 1.7 | 20.55 | 24708 | 23402 | 1257 | 99.89 | 0.15801 | 0.15653 | 0.18704 | RANDOM | 15.678 |
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] | |
-0.16 | -0.2 | 0.36 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.091 |
r_dihedral_angle_4_deg | 21.974 |
r_dihedral_angle_3_deg | 12.658 |
r_dihedral_angle_1_deg | 6.325 |
r_scangle_it | 4.303 |
r_scbond_it | 2.61 |
r_mcangle_it | 1.685 |
r_angle_refined_deg | 1.482 |
r_mcbond_it | 0.917 |
r_chiral_restr | 0.109 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1629 |
Nucleic Acid Atoms | |
Solvent Atoms | 168 |
Heterogen Atoms | 22 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrysalisPro | data collection |
CrysalisPro | data reduction |