2A5H
2.1 Angstrom X-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale SB4, with Michaelis analog (L-alpha-lysine external aldimine form of pyridoxal-5'-phosphate).
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 300 | sodium N-2-hydroxy-ethylpiperazine-N'--3-propage sulfonic acid (EPPS, or HEPPS), sodium malonaate, L-alpha-lysine, dithiothreitol, polyethylene glycol 200, polyethylene glycol 8000, s-adenosylmethionine, iron-II-sulfate, , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K |
2 | VAPOR DIFFUSION, HANGING DROP | 8 | 300 | sodium N-2-hydroxy-ethylpiperazine-N'--3-propage sulfonic acid (EPPS, or HEPPS), sodium malonaate, L-alpha-lysine, dithiothreitol, polyethylene glycol 200, polyethylene glycol 8000, s-adenosylmethionine, iron-II-sulfate, , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 118.89 | α = 90 |
b = 92.926 | β = 96.74 |
c = 177.735 | 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 315 | monochromator with Si (111) crystal | 2003-04-09 | M | SINGLE WAVELENGTH | |||||
2 | 2 | x-ray | 100 | CCD | ADSC QUANTUM 4 | monochromator with Si(111) double-crystal | 2003-03-28 | M |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X25 | 0.9742 | NSLS | X25 |
2 | SYNCHROTRON | APS BEAMLINE 17-ID | 0.9792 | APS | 17-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 | |||||||
1,2 | 2.1 | 50 | 81.53 | 0.103 | 0.103 | 2 | 3 | 83957 | 83957 |
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) | ||||||||||
1,2 | 2.1 | 2.18 | 62.3 | 0.265 | 0.265 | 2.97 | 2.2 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 2.1 | 50 | 83957 | 83957 | 7437 | 81.53 | 0.18732 | 0.18396 | 0.22485 | RANDOM | 33.824 |
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] | |
0.3 | -1.71 | 3.3 | -4.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.993 |
r_dihedral_angle_4_deg | 20.774 |
r_dihedral_angle_3_deg | 20.343 |
r_dihedral_angle_1_deg | 7.18 |
r_angle_refined_deg | 3.086 |
r_scangle_it | 2.362 |
r_scbond_it | 1.635 |
r_mcangle_it | 0.861 |
r_mcbond_it | 0.582 |
r_symmetry_hbond_refined | 0.393 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 12990 |
Nucleic Acid Atoms | |
Solvent Atoms | 608 |
Heterogen Atoms | 264 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CBASS | data collection |
MX | data reduction |
JBluIce-EPICS | data collection |
SCALEPACK | data scaling |
SOLVE | phasing |