3R1Z
Crystal structure of NYSGRC enolase target 200555, a putative dipeptide epimerase from Francisella philomiragia : Complex with L-Ala-L-Glu and L-Ala-D-Glu
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | vapour diffusion, sitting drop | 5.6 | 294 | Protein: 10 mM HEPES pH 7.5, 150 mM Nacl, 10% glycerol, 5 mM DTT; Reservoir: 2M Ammonium Sulfate, 100 mM NaCitrate, 200 mM KNaTartrate; Soak: 2.2 M Ammonium sulfate, 100 mM MES pH 6.0, 18% glycerol, 50mM MgSO4, 25 mM L-Ala-L-Glu, 30 min, vapour diffusion, sitting drop, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.22 | 61.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 121.19 | α = 90 |
b = 121.19 | β = 90 |
c = 149.02 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 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 | 98 | CCD | RAYONIX MX225HE | Undulator Source | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.97905 | APS | 31-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.9 | 50 | 97.9 | 0.097 | 0.097 | 16.4 | 12.5 | 85703 | 85703 | 19.31 |
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 | 1.9 | 2 | 92.5 | 0.38 | 0.38 | 5.8 | 12.1 | 3006 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | 1.9 | 29.69 | 84359 | 84359 | 4221 | 96.28 | 0.1585 | 0.1585 | 0.1571 | 0.1854 | Random | 24.6422 |
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] | |
0.258 | 0.258 | 0.7469 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.337 |
f_angle_d | 1.242 |
f_chiral_restr | 0.1 |
f_bond_d | 0.008 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5605 |
Nucleic Acid Atoms | |
Solvent Atoms | 708 |
Heterogen Atoms | 84 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
MAR345dtb | data collection |
MOSFLM | data reduction |
SCALEPACK | data scaling |
PHENIX | phasing |