8C36
Light-adapted 2.0 Angstrom crystal structure of H132A variant of cobalamin binding domain belonging to a light-dependent transcription regulator TtCarH obtained under aerobic conditions
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.8 | 293 | 0.1 M ammonium sulfate, 0.1 M sodium citrate pH 5.8, 16% w/v PEG 4000, 20% v/v glycerol |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.46 | 49.99 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 63.405 | α = 90 |
b = 70.664 | β = 90 |
c = 203.687 | 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 EIGER2 X 16M | 2021-09-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9763 | Diamond | I03 |
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 | 67.9 | 100 | 1 | 10.3 | 13.5 | 62906 |
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 | 2.05 | 100 | 0.6 | 1 | 13.5 |
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 | 8C35 | 2 | 66.85 | 59761 | 3060 | 99.94 | 0.18293 | 0.18113 | 0.2183 | RANDOM | 45.436 |
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] | |
2.79 | -0.16 | -2.63 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 16.303 |
r_dihedral_angle_2_deg | 10.218 |
r_long_range_B_refined | 8.144 |
r_long_range_B_other | 8.048 |
r_dihedral_angle_1_deg | 5.992 |
r_scangle_other | 5.373 |
r_scbond_it | 3.482 |
r_scbond_other | 3.482 |
r_mcangle_it | 3.24 |
r_mcangle_other | 3.24 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5838 |
Nucleic Acid Atoms | |
Solvent Atoms | 475 |
Heterogen Atoms | 364 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
DIALS | data scaling |
PHASER | phasing |