3IJL
Structure of dipeptide epimerase from Bacteroides thetaiotaomicron complexed with L-Pro-D-Glu; nonproductive substrate binding.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3IJI | PDB entry 3IJI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 293 | 17% PEG 10000, 0.1M Bis-Tris, 0.1M ammonium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.84 | 56.71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 141.897 | α = 90 |
b = 100.074 | β = 90.34 |
c = 60.075 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 QUANTUM 4 | 2008-12-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4A | 0.97915 | NSLS | X4A |
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 | 1.5 | 25 | 97.1 | 0.086 | 129985 | 129985 | 18.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | PDB entry 3IJI | 1.5 | 24.91 | 129985 | 129985 | 6545 | 97.1 | 0.192 | 0.192 | 0.205 | RANDOM | 20.3 |
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] | |
1.01 | -0.5 | -3.77 | 2.75 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.1 |
c_scangle_it | 2.51 |
c_scbond_it | 1.71 |
c_mcangle_it | 1.5 |
c_angle_deg | 1.3 |
c_mcbond_it | 0.97 |
c_improper_angle_d | 0.84 |
c_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5224 |
Nucleic Acid Atoms | |
Solvent Atoms | 648 |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
BALBES | phasing |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |