7L47
The internal aldimine form of the beta-K167T mutant Tryptophan Synthase from Salmonella at 1.55 Angstrom resolution with cesium ion at the metal coordination site
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.6 | 298 | 50 mM Bicine-CsOH, 10% PEG 8,000, 4 mM Spermine, pH 7.6 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.58 | 52.34 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 181.979 | α = 90 |
b = 59.33 | β = 94.34 |
c = 67.07 | 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 | IMAGE PLATE | RIGAKU RAXIS IV++ | VariMax HighFlux | 2020-03-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.55 | 90.729 | 96.6 | 0.06 | 0.06 | 0.091 | 0.05 | 8.4 | 3 | 99916 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.55 | 1.63 | 77.3 | 0.551 | 0.551 | 0.768 | 0.477 | 1.3 | 2.2 |
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 | 7K0B | 1.55 | 38.94 | 94796 | 5064 | 96.47 | 0.1891 | 0.1878 | 0.2123 | RANDOM | 23.514 |
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] | |
-0.09 | -0.07 | 0.29 | -0.18 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.396 |
r_dihedral_angle_4_deg | 18.732 |
r_dihedral_angle_3_deg | 12.709 |
r_dihedral_angle_1_deg | 6.385 |
r_angle_refined_deg | 1.59 |
r_chiral_restr | 0.102 |
r_bond_refined_d | 0.009 |
r_gen_planes_refined | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4879 |
Nucleic Acid Atoms | |
Solvent Atoms | 727 |
Heterogen Atoms | 124 |
Software
Software | |
---|---|
Software Name | Purpose |
iMOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |
DM | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |