7C0X
Crystal structure of a dinucleotide-binding protein (T240A) of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 0.2M ammonium phosphate, 0.1M sodium cacodylate pH 6.5, 30% PEG 8000 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.66 | 53.79 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 66.64 | α = 90 |
b = 58.08 | β = 95.34 |
c = 122.02 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 1 21 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 | IMAGE PLATE | RIGAKU RAXIS IV++ | VariMax HF | 2019-07-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
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 | 1.77 | 60.75 | 93.1 | 0.17 | 0.192 | 0.089 | 0.974 | 6.6 | 4.2 | 83929 |
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 | 1.77 | 1.81 | 81.7 | 0.486 | 0.554 | 0.262 | 0.764 | 4.1 |
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 | 7C0F | 1.77 | 60.75 | 79825 | 4086 | 92.85 | 0.1876 | 0.1856 | 0.2264 | RANDOM | 20.411 |
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] | |
-7.8 | 2.21 | -1.52 | 9.31 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.806 |
r_dihedral_angle_4_deg | 17.025 |
r_dihedral_angle_3_deg | 15.199 |
r_dihedral_angle_1_deg | 6.342 |
r_angle_refined_deg | 2.025 |
r_angle_other_deg | 1.486 |
r_chiral_restr | 0.108 |
r_bond_refined_d | 0.016 |
r_gen_planes_refined | 0.013 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6080 |
Nucleic Acid Atoms | |
Solvent Atoms | 756 |
Heterogen Atoms | 152 |
Software
Software | |
---|---|
Software Name | Purpose |
HKL-3000 | data collection |
MOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |
REFMAC | refinement |
PDB_EXTRACT | data extraction |