6T9R
Aplysia californica AChBP in complex with a cytisine derivative
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 6QKK |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 295.15 | Starting protein concentration 12.5 mg/ml + 6 mM ligand BS82. Crystallised as hanging drops, the drop containing 1.5 ul protein, 0.2 ul reservoir (0.8 M NaH2PO4, 0.8 M KH2PO4, 10% glycerol, 0.1 M HEPES pH 7.0) and 0.3 ul microseeds from cytisine bound AChBP crystals (grown as sitting drops in 0.8 M NaH2PO4, 0.8 M KH2PO4, 0.1 M HEPES pH 7.5). |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.14 | 60.87 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 209.466 | α = 90 |
b = 132.874 | β = 102.524 |
c = 131.086 | γ = 90 |
Symmetry | |
---|---|
Space Group | C 1 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 | 100 | PIXEL | DECTRIS EIGER2 X 16M | 2019-08-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.976 | Diamond | I03 |
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 | 1.72 | 127.97 | 95.5 | 0.07 | 0.095 | 0.064 | 0.993 | 7.6 | 3.5 | 353432 | 25.07 |
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 | 1.72 | 1.75 | 66.6 | 0.82 | 1.138 | 0.787 | 0.435 | 0.6 | 2.1 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6QKK | 1.72 | 111.666 | 353365 | 17388 | 95.459 | 0.163 | 0.1619 | 0.1922 | 30.393 |
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] | |
-2.078 | -0.075 | 2.651 | -0.491 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.528 |
r_dihedral_angle_4_deg | 20.452 |
r_dihedral_angle_1_deg | 19.702 |
r_dihedral_angle_3_deg | 13.707 |
r_lrange_it | 8.358 |
r_lrange_other | 8.106 |
r_scangle_it | 6.038 |
r_scangle_other | 6.038 |
r_scbond_it | 4.143 |
r_scbond_other | 4.143 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 16425 |
Nucleic Acid Atoms | |
Solvent Atoms | 2899 |
Heterogen Atoms | 636 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
Aimless | data scaling |
PHASER | phasing |