7VBR
Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxI
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 0.1M Bis-Tris (PH 6.5), 2% (v/v) Tacsimate (PH 6.0), 20% (w/v) PEG 3350 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.4 | 48.69 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 64.403 | α = 81.75 |
b = 64.45 | β = 73.705 |
c = 76.988 | γ = 74.825 |
Symmetry | |
---|---|
Space Group | P 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 EIGER X 4M | 2020-11-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-1A | 1.1 | Photon Factory | BL-1A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.1 | 49.32 | 97.7 | 0.081 | 0.996 | 9.1 | 3.7 | 65297 | 31.6 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.1 | 2.15 | 0.711 | 0.601 | 1.5 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | FREE R-VALUE | 5zm2 | 2.1 | 49.32 | 1.76 | 65284 | 1999 | 97.59 | 0.2101 | 0.2087 | 0.254 | 37.09 |
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 | 16.6076 |
f_angle_d | 0.9106 |
f_chiral_restr | 0.0533 |
f_bond_d | 0.0081 |
f_plane_restr | 0.0067 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 7383 |
Nucleic Acid Atoms | |
Solvent Atoms | 376 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |