6OV8
2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B from Escherichia coli str. K-12 substr. MG1655
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 292 | Protein: 8.2 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, 1mM Zn, 1mM Mn Screen: Classics II (F10), 0.2M Sodium chloride, 0.1M BIS-TRIS pH 5.5, 25% (w/v) PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.51 | 50.96 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 114.857 | α = 90 |
b = 148.19 | β = 90 |
c = 165.01 | γ = 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 | 100 | CCD | MARMOSAIC 300 mm CCD | C(111) | 2019-04-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.9787 | 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 | 2.6 | 30 | 100 | 0.136 | 0.136 | 0.149 | 0.059 | 14.4 | 6.2 | 85965 | -3 | 38.8 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.6 | 2.64 | 100 | 0.79 | 0.79 | 0.861 | 0.341 | 0.837 | 2.5 | 6.3 |
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 | 6OAD | 2.61 | 29.76 | 81597 | 4240 | 99.56 | 0.18411 | 0.1813 | 0.2376 | RANDOM | 41.039 |
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] | |
3.14 | 1.36 | -4.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 24.819 |
r_dihedral_angle_3_deg | 11.52 |
r_dihedral_angle_4_deg | 10.238 |
r_dihedral_angle_1_deg | 4.224 |
r_long_range_B_refined | 3.245 |
r_long_range_B_other | 3.212 |
r_scangle_other | 1.796 |
r_mcangle_it | 1.708 |
r_mcangle_other | 1.708 |
r_scbond_it | 1.112 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 19510 |
Nucleic Acid Atoms | |
Solvent Atoms | 614 |
Heterogen Atoms | 33 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHASER | phasing |