8UXS
KLHDC2 ubiquitin ligase in complex with a novel small-molecule
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 6DO3 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 298.15 | 0.03 M MgCl2*6H2O, 0.03 M CaCl2*2H2O, 10% (w/v) PEG 20000, 20% (v/v) PEG MME, 0.1 M Tris (base)/ bicine pH 8.5 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.15 | 42.81 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 44.381 | α = 90 |
b = 88.165 | β = 104.39 |
c = 88.512 | 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 | PIXEL | DECTRIS EIGER2 S 9M | 2023-06-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.1 | 1.0 | ALS | 8.2.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.44 | 44.08 | 70.05 | 0.064 | 0.076 | 0.041 | 2967.5 | 3.1 | 85458 | 25.45 |
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 | 1.44 | 2.071 | 99.48 | 0.1776 | 0.2113 | 0.1132 | 0.597 | 3.2 | 3.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2 | 44.08 | 1.44 | 85458 | 2273 | 97.31 | 0.1671 | 0.1661 | 0.2018 | 28.9 |
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 | 6.1796 |
f_angle_d | 0.575 |
f_chiral_restr | 0.0442 |
f_plane_restr | 0.0036 |
f_bond_d | 0.0023 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5184 |
Nucleic Acid Atoms | |
Solvent Atoms | 261 |
Heterogen Atoms | 52 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
DIALS | data scaling |
PHENIX | phasing |
Coot | model building |