6A4R
Crystal structure of aspartate bound peptidase E from Salmonella enterica
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 5.5 | 294 | 0.1 M Bis-tris pH 5.5, 0.2 M Sodium chloride, 31 % Peg 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.79 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.155 | α = 90 |
b = 42.889 | β = 107.02 |
c = 89.29 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | IMAGE PLATE | MAR scanner 345 mm plate | mirrors | 2018-06-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | RRCAT INDUS-2 BEAMLINE PX-BL21 | 0.97949 | RRCAT INDUS-2 | PX-BL21 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.827 | 45.34 | 96.2 | 0.057 | 0.07 | 0.041 | 0.997 | 13.4 | 2.9 | 41754 | 19.3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.83 | 1.87 | 79.5 | 0.47 | 0.601 | 0.369 | 0.74 | 1.9 | 2.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1FY2 | 1.828 | 41.605 | 1.34 | 41715 | 2062 | 95.84 | 0.1902 | 0.189 | 0.2126 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.411 |
f_angle_d | 0.643 |
f_chiral_restr | 0.048 |
f_plane_restr | 0.005 |
f_bond_d | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3526 |
Nucleic Acid Atoms | |
Solvent Atoms | 269 |
Heterogen Atoms | 18 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
Coot | model building |
PHASER | phasing |
Aimless | data scaling |
XDS | data reduction |
MAR345dtb | data collection |