2XE4
Structure of Oligopeptidase B from Leishmania major
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.2 | PROTEIN WAS DIALYZED INTO 50 MM TRIS, PH 8.0 AND INCUBATED WITH 10 MM ANTIPAIN FOR 30 MINS. THIS WAS MIXED IN A 1:1 RATIO WITH 25% 1,2 PROPANEDIOL, 10% GLYCEROL, 5 % PEG300 AND 0.1 M PHOSPHATE CITRATE, PH 4.2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.2 | 71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 95.478 | α = 90 |
b = 142.776 | β = 90 |
c = 208.919 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 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 | 103 | IMAGE PLATE | MARRESEARCH | MIRRORS | 2008-06-10 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 103 | CCD | MARRESEARCH | M |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | |||
2 | SYNCHROTRON | ESRF BEAMLINE BM14 | ESRF | BM14 |
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 | 1.65 | 32 | 98.4 | 0.06 | 8.8 | 3.3 | 167772 | 1.5 | 29.5 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.65 | 1.71 | 100 | 0.46 | 1.7 | 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 | SAD | THROUGHOUT | NONE | 1.65 | 117.851 | 167169 | 8321 | 98.007 | 0.142 | 0.1403 | 0.178 | RANDOM | 41.338 |
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] | |
2.673 | -1.71 | -0.963 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.738 |
r_dihedral_angle_4_deg | 15.532 |
r_dihedral_angle_3_deg | 12.49 |
r_scangle_it | 9.512 |
r_scbond_it | 6.794 |
r_dihedral_angle_1_deg | 6.661 |
r_mcangle_it | 4.118 |
r_rigid_bond_restr | 3.903 |
r_mcbond_it | 2.833 |
r_angle_refined_deg | 2.353 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5809 |
Nucleic Acid Atoms | |
Solvent Atoms | 721 |
Heterogen Atoms | 326 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
d*TREK | data reduction |
SCALA | data scaling |
autoSHARP | phasing |
SHELXCD | phasing |
SHELXD | phasing |