6XJ4
Triuret Hydrolase (TrtA) from Herbaspirillum sp. BH-1 C162S bound with biuret
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 6XIX | PDB entry 6XIX |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 9 | 291 | 1uL 10 mg/mL TrtA + 1 uL 26% w/v PEG6000, 0.1 M Bis-Tris propane, 30 mM biuret, pH 9 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.15 | 42.86 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 51.63 | α = 90 |
b = 114.18 | β = 90 |
c = 141.47 | γ = 90 |
Symmetry | |
---|---|
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 | PIXEL | DECTRIS EIGER X 16M | 2019-04-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 0.992 | APS | 23-ID-B |
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 | 1.78 | 57.09 | 99.8 | 0.062 | 12.44 | 3.85 | 80968 |
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 | 1.78 | 1.88 | 99.9 | 0.369 | 4.26 | 3.77 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 6XIX | 1.78 | 57.09 | 80968 | 4049 | 99.928 | 0.157 | 0.1557 | 0.1872 | 27.334 |
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] | |
-1.077 | -1.102 | 2.178 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.407 |
r_dihedral_angle_4_deg | 18.523 |
r_dihedral_angle_3_deg | 12.863 |
r_dihedral_angle_1_deg | 6.519 |
r_lrange_it | 6.51 |
r_lrange_other | 6.407 |
r_scangle_it | 5.693 |
r_scangle_other | 5.693 |
r_scbond_it | 3.85 |
r_scbond_other | 3.85 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6698 |
Nucleic Acid Atoms | |
Solvent Atoms | 412 |
Heterogen Atoms | 27 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
Coot | model building |
XDS | data scaling |
MOLREP | phasing |
XDS | data reduction |