8RZ6
SeMet derivative structure of the condensation domain TomBC from the Tomaymycin non-ribosomal peptide synthetase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 100 mM Tris pH 8.5, 3.0 M KFormate, with 25% glycerol used as cryoprotectant |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.43 | 64.11 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 123.35 | α = 90 |
b = 160.87 | β = 125.11 |
c = 100.15 | γ = 90 |
Symmetry | |
---|---|
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 | PIXEL | DECTRIS PILATUS 6M | 2015-07-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.979733 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | 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 | 2.3 | 48.91 | 99.1 | 0.994 | 9.9 | 10.58 | 139112 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.3 | 2.4 | 98.7 | 0.747 | 2.1 | 10.82 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.3 | 48.91 | 1.36 | 70285 | 3515 | 99.41 | 0.1746 | 0.1724 | 0.2164 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 5.845 |
f_angle_d | 1.011 |
f_chiral_restr | 0.053 |
f_bond_d | 0.011 |
f_plane_restr | 0.011 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6825 |
Nucleic Acid Atoms | |
Solvent Atoms | 586 |
Heterogen Atoms | 34 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
AutoSol | phasing |
XDS | data reduction |
Aimless | data scaling |