6X1I
Two-Component D3 Assembly Constructed by Fusing Symmetric Oligomers to Coiled Coils
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 277.15 | Reagent Well: - 10ul of Silver Bullets additive screen reagent B9: 0.25% w/v Hexamminecobalt(III) chloride, 0.25% w/v Salicylamide, 0.25% w/v Sulfanilamide, 0.25% w/v Vanillic acid, 0.02 M HEPES sodium pH 6.8 - 90ul of crystallization reagent: 0.10 M Sodium Acetate pH 5.4, 66% MPD Drop: - 2:1 protein sample to well reagent ratio - Protein sample: 2.8mg/ml of purified protein in 0.5M NaCl, 5% Glycerol, 2.8mM beta-mercaptoethanol, 50 mM Tris pH 7.5, 5mM MgCl2 sample buffer |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.52 | 65.08 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 146.34 | α = 90 |
b = 146.34 | β = 90 |
c = 146.34 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 43 3 2 |
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 PILATUS 6M-F | 2015-11-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.9790 | APS | 24-ID-C |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 4.32 | 84.5 | 99.7 | 0.095 | 0.099 | 1 | 14.4 | 17.657 | 3945 | 237.211 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 4.32 | 4.44 | 96.9 | 2.374 | 2.449 | 0.411 | 1.3 | 16.765 |
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 | 1WY1, 3DXO | 4.32 | 84.49 | 1.35 | 3910 | 391 | 99.47 | 0.2796 | 0.2778 | 0.2926 | 267.69 |
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 | 14.7134 |
f_angle_d | 0.9202 |
f_chiral_restr | 0.0522 |
f_bond_d | 0.0042 |
f_plane_restr | 0.0039 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2507 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |