6CX8
Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Vibrio cholerae in complex with manganese ions.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4NCZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | 0.2 M Trimethylamine N-oxide, 0.1 M Tris, 20% w/v PEG2000 MME |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.74 | 55.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 157.645 | α = 90 |
b = 135.267 | β = 118.58 |
c = 73.675 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | RAYONIX MX-300 | Beryllium Lenses | 2016-03-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
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 | 2.4 | 30 | 94.3 | 0.063 | 26.7 | 3.4 | 49284 |
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 | 2.4 | 2.44 | 97.7 | 0.52 | 2.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 4NCZ | 2.41 | 30 | 46921 | 2363 | 93.68 | 0.17346 | 0.17137 | 0.21319 | RANDOM | 56.615 |
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] | |
-0.97 | -1.61 | 0.13 | 1.63 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.586 |
r_dihedral_angle_4_deg | 14.832 |
r_dihedral_angle_3_deg | 12.755 |
r_long_range_B_other | 9.226 |
r_long_range_B_refined | 9.222 |
r_scangle_other | 7.547 |
r_mcangle_it | 5.626 |
r_mcangle_other | 5.626 |
r_scbond_it | 5.592 |
r_scbond_other | 5.591 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8616 |
Nucleic Acid Atoms | |
Solvent Atoms | 206 |
Heterogen Atoms | 43 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
BLU-MAX | data collection |
HKL-3000 | data scaling |
HKL-3000 | data reduction |
PHASER | phasing |
Coot | model building |