6OAD
2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B from Escherichia coli str. K-12 substr. MG1655.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3IJ3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 292 | Protein: 6.0 mg/ml, 0.01M Tris pH 8.3; Screen: PEGs II (H8), 0.2M Calcium acetate, 0.1M HEPES pH 7.5, 10% (w/v) PEG 8000. Cryo: reservoir + 20% Ethylene glycol. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 150.667 | α = 90 |
b = 114.761 | β = 92.02 |
c = 161.171 | 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 | CCD | MARMOSAIC 300 mm CCD | C(111) | 2019-02-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.05 | 30 | 98.8 | 0.098 | 0.098 | 0.112 | 0.054 | 11.9 | 4.1 | 338775 | -3 | 30.9 |
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) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 2.05 | 2.09 | 96.4 | 0.791 | 0.791 | 0.905 | 0.437 | 0.761 | 1.9 | 4.1 |
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 | 3IJ3 | 2.05 | 29.88 | 321648 | 16698 | 98.62 | 0.17398 | 0.17185 | 0.21473 | RANDOM | 37.118 |
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] | |
1.68 | -2.3 | 0.94 | -2.46 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 22.462 |
r_dihedral_angle_4_deg | 10.639 |
r_dihedral_angle_3_deg | 9.454 |
r_long_range_B_refined | 6.735 |
r_long_range_B_other | 6.735 |
r_dihedral_angle_1_deg | 3.09 |
r_scangle_other | 1.718 |
r_angle_refined_deg | 1.473 |
r_scbond_it | 1.471 |
r_scbond_other | 1.471 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 38883 |
Nucleic Acid Atoms | |
Solvent Atoms | 3385 |
Heterogen Atoms | 323 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
MoRDa | phasing |