4BP8
Oligopeptidase B from Trypanosoma brucei - open form
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 9 | 9% (W/V) POLYETHYLENE GLYCOL 6000, 1M LITHIUM CHLORIDE, 100MM BIS-TRIS PROPANE, PH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.88 | 57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 124.14 | α = 90 |
b = 124.14 | β = 90 |
c = 249.14 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 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 | ADSC CCD | MIRRORS | 2008-11-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | ESRF | ID29 |
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 | 2.4 | 66 | 99.3 | 0.17 | 18.6 | 34.6 | 86984 | -3 | 53.3 |
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 | 2.4 | 2.53 | 95.6 | 1.5 | 2 | 22.2 |
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 | SAD | THROUGHOUT | NONE | 2.4 | 65.73 | 83463 | 3521 | 99.31 | 0.18625 | 0.18402 | 0.23885 | RANDOM | 46.311 |
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] | |
1.95 | 0.98 | 1.95 | -2.93 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.226 |
r_dihedral_angle_4_deg | 19.688 |
r_dihedral_angle_3_deg | 18.324 |
r_dihedral_angle_1_deg | 7.639 |
r_scangle_it | 3.754 |
r_scbond_it | 2.322 |
r_angle_refined_deg | 1.721 |
r_mcangle_it | 1.325 |
r_mcbond_it | 0.677 |
r_chiral_restr | 0.132 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11302 |
Nucleic Acid Atoms | |
Solvent Atoms | 778 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
SOLVE | phasing |
RESOLVE | phasing |
REFMAC | refinement |