4FUU
Crystal structure of a leucine aminopeptidase precursor (BT_2548) from Bacteroides thetaiotaomicron VPI-5482 at 1.30 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 20.00% polyethylene glycol 3350, 0.200M ammonium dihydrogen phosphate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.236 | α = 65.47 |
b = 41.582 | β = 80.43 |
c = 48.528 | γ = 78.68 |
Symmetry | |
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Space Group | P 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 QUANTUM 315 | KOHZU: Double Crystal Si(111) | 2011-10-16 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | 0.9537,0.9796,0.9793 | ALS | 8.2.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.3 | 27.993 | 93.6 | 0.055 | 7.1 | 1.9 | 64313 | 64313 | 12.234 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.3 | 1.33 | 91.3 | 0.435 | 0.435 | 1.9 | 1.9 | 4638 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 1.3 | 27.993 | 64273 | 3265 | 93.53 | 0.12 | 0.1181 | 0.1566 | RANDOM | 17.9771 |
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] | |
-0.17 | -0.14 | 0.01 | -0.06 | 0.6 | -0.22 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.544 |
r_dihedral_angle_4_deg | 21.435 |
r_sphericity_free | 12.521 |
r_dihedral_angle_3_deg | 11.458 |
r_scangle_it | 6.63 |
r_dihedral_angle_1_deg | 5.811 |
r_sphericity_bonded | 5.551 |
r_scbond_it | 4.76 |
r_mcangle_it | 3.525 |
r_mcbond_it | 2.485 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2259 |
Nucleic Acid Atoms | |
Solvent Atoms | 329 |
Heterogen Atoms | 22 |
Software
Software | |
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Software Name | Purpose |
MolProbity | model building |
PDB_EXTRACT | data extraction |
SHELX | phasing |
SHARP | phasing |
SCALA | data scaling |
REFMAC | refinement |
MOSFLM | data reduction |
SHELXD | phasing |