3IFE
1.55 Angstrom Resolution Crystal Structure of Peptidase T (pepT-1) from Bacillus anthracis str. 'Ames Ancestor'.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1FNO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 295 | Protein solution: 7.5mg/mL, 0.25M NaCl, Tris-HCl pH(8.3); Screen solution: JCSG+, E2, 0.2M NaCl, 2M Ammonium sulfate, 0.1M Na-Cacodilate pH(6.5) VAPOR DIFFUSION, SITTING DROP, temperature 295K; Cryo: 25% Sucrose, 1.8M Ammonium sulfate. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.68 | 54.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.216 | α = 90 |
b = 142.739 | β = 90 |
c = 40.993 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | MARMOSAIC 300 mm CCD | Beryllium lenses | 2009-07-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
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 | 1.55 | 30 | 99.9 | 0.068 | 25.8 | 7.3 | 77209 | 77209 | -3 | 21 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.55 | 1.58 | 99.3 | 0.554 | 3.3 | 6.5 | 3814 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1fno | 1.55 | 29.11 | 73110 | 73110 | 3863 | 99.94 | 0.14954 | 0.14954 | 0.14836 | 0.17173 | RANDOM | 12.404 |
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] | |
-1.09 | -0.36 | 1.46 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.925 |
r_dihedral_angle_4_deg | 13.661 |
r_dihedral_angle_3_deg | 9.079 |
r_scangle_it | 4.329 |
r_dihedral_angle_1_deg | 3.19 |
r_scbond_it | 2.664 |
r_angle_refined_deg | 1.493 |
r_mcangle_it | 1.481 |
r_angle_other_deg | 0.879 |
r_mcbond_it | 0.854 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3282 |
Nucleic Acid Atoms | |
Solvent Atoms | 586 |
Heterogen Atoms | 59 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
CRANK | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |