5O8F
Structure of a chimaeric beta3-alpha5 GABAA receptor in complex with nanobody Nb25 and pregnanolone
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4COF | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 277 | 14% PEG 6000, 0.1M N-(2-Acetamido)iminodiacetic acid (ADA), 7.6 mM 4-Cyclohexyl-1-Butyl-beta-D-Maltoside (CYMAL-4) |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.5 | 64.9 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 290.102 | α = 90 |
| b = 290.102 | β = 90 |
| c = 290.102 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 2 3 |
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 PILATUS3 6M | 2015-07-26 | 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) | R Merge I (Observed) | 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 | 3.19 | 49.752 | 100 | 0.621 | 0.131 | 0.986 | 6.8 | 30.4 | 66928 | 68.2 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 3.19 | 3.31 | 100 | 3.131 | 0.609 | 0.215 | 1.2 | 25.5 | |||||||||||
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 | 4COF | 3.2 | 205.13 | 63621 | 3304 | 99.96 | 0.23296 | 0.23246 | 0.2424 | RANDOM | 70.752 | ||||||
| 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 |
| r_dihedral_angle_2_deg | 29.33 |
| r_dihedral_angle_3_deg | 12.369 |
| r_dihedral_angle_4_deg | 11.664 |
| r_dihedral_angle_1_deg | 5.452 |
| r_long_range_B_refined | 5.237 |
| r_long_range_B_other | 5.237 |
| r_scangle_other | 2.002 |
| r_mcangle_it | 1.915 |
| r_mcangle_other | 1.915 |
| r_scbond_it | 1.164 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 18217 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | 600 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
| Coot | model building |
