8FD0
Crystal structure of bovine rod opsin in complex with a nanobody
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.16 | 277.15 | 25% PEG 600 0.1 M Tricine pH 8.16 5 mM EDTA 5 mM beta mercaptoethanol 10 mM hydroxylamine 50 mM CYGLU-4 * reservoir solution contained 30% PEG 600 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.54 | 72.93 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 120.065 | α = 90 |
b = 120.065 | β = 90 |
c = 230.943 | γ = 120 |
Symmetry | |
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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 | 100 | PIXEL | DECTRIS EIGER X 16M | 2022-02-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-E | 0.97918 | APS | 24-ID-E |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 3.71 | 50 | 99.9 | 0.055 | 0.999 | 15.83 | 10 | 20961 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.71 | 3.94 | 3.659 | 0.221 | 0.65 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | FOURIER SYNTHESIS | THROUGHOUT | 3.71 | 47.41 | 19956 | 1033 | 99.68 | 0.2921 | 0.2919 | 0.2953 | RANDOM | 230.952 |
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] | |
0.44 | 0.22 | 0.44 | -1.42 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 12.946 |
r_dihedral_angle_2_deg | 7.797 |
r_dihedral_angle_1_deg | 5.488 |
r_angle_refined_deg | 0.67 |
r_angle_other_deg | 0.246 |
r_chiral_restr | 0.037 |
r_bond_refined_d | 0.002 |
r_gen_planes_refined | 0.002 |
r_bond_other_d | 0.001 |
r_gen_planes_other | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6629 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 203 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
XDS | data scaling |
REFMAC | phasing |