3GJY
Crystal structure of a probable spermidine synthase from Corynebacterium glutamicum ATCC 13032
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 289 | 0.2M Potassium sodium tartrate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.13 | 42.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.909 | α = 90 |
b = 65.009 | β = 90 |
c = 87.308 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | Mirror | 2008-11-23 | M | SAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97915 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.47 | 23 | 99.4 | 0.068 | 43.5 | 8.2 | 51371 | 51371 |
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) | |||||||||||
1.47 | 1.5 | 95.6 | 0.482 | 2.88 | 6.6 | 2418 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.47 | 22.62 | 48639 | 48639 | 2614 | 99.28 | 0.1588 | 0.1588 | 0.15704 | 0.19152 | RANDOM | 20.23 |
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] | |
-0.01 | 0.04 | -0.02 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.834 |
r_dihedral_angle_4_deg | 17.204 |
r_dihedral_angle_3_deg | 12.74 |
r_sphericity_free | 6.758 |
r_dihedral_angle_1_deg | 6.159 |
r_scangle_it | 4.535 |
r_sphericity_bonded | 4.15 |
r_scbond_it | 3.14 |
r_mcangle_it | 2.231 |
r_rigid_bond_restr | 1.702 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2251 |
Nucleic Acid Atoms | |
Solvent Atoms | 388 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
SBC-Collect | data collection |
SHELXD | phasing |
MLPHARE | phasing |
DM | model building |
ARP/wARP | model building |
HKL-3000 | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
DM | phasing |