7Y8V
Crystal structure of AlbEF homolog mutant (AlbF-H54A/H58A) from Quasibacillus thermotolerans
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 293 | sodium/potassium phosphate |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.63 | 66.09 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 136.423 | α = 90 |
b = 136.423 | β = 90 |
c = 119.001 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 31 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 | 95 | PIXEL | DECTRIS PILATUS3 S 6M | 2019-12-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1.00000 | Photon Factory | BL-5A |
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 | 2.3 | 44.84 | 99.8 | 0.048 | 0.05 | 0.016 | 1 | 25.3 | 10.2 | 57022 | 50.47 |
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 | 2.3 | 2.36 | 99.7 | 0.458 | 0.483 | 0.153 | 0.971 | 4.6 | 9.9 |
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 | 7Y8U | 2.3 | 41.92 | 1.1 | 56973 | 2681 | 99.8 | 0.2014 | 0.1999 | 0.2331 | 75.61 |
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 | 12.712 |
f_angle_d | 0.506 |
f_chiral_restr | 0.0414 |
f_plane_restr | 0.0035 |
f_bond_d | 0.0028 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5863 |
Nucleic Acid Atoms | |
Solvent Atoms | 58 |
Heterogen Atoms | 63 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |