9J0U
Crystal structure of monomeric PLP-dependent transaminase from Desulfobacula toluolica in F 41 3 2 space group
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 288 | 400mM NaNitrate, 0.1M Bis-tris propane pH 6.5, 20% PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.08 | 75.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 250.089 | α = 90 |
b = 250.089 | β = 90 |
c = 250.089 | γ = 90 |
Symmetry | |
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Space Group | F 41 3 2 |
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 | 2021-07-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 0.89999 | SPring-8 | BL41XU |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.58 | 144.39 | 100 | 0.191 | 0.192 | 0.023 | 0.998 | 17.3 | 66.9 | 21699 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.58 | 2.69 | 100 | 9.059 | 9.174 | 1.437 | 0.446 | 37.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.58 | 88.58 | 20573 | 1096 | 99.97 | 0.21116 | 0.20912 | 0.25274 | RANDOM | 98.156 |
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 | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.086 |
r_dihedral_angle_4_deg | 26.33 |
r_dihedral_angle_3_deg | 23.405 |
r_long_range_B_refined | 15.752 |
r_mcangle_it | 11.131 |
r_scbond_it | 10.553 |
r_dihedral_angle_1_deg | 10.173 |
r_mcbond_it | 8.228 |
r_angle_refined_deg | 3.474 |
r_chiral_restr | 0.293 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2238 |
Nucleic Acid Atoms | |
Solvent Atoms | 15 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
DIALS | data reduction |
MOLREP | phasing |
PDB_EXTRACT | data extraction |