6T2F
Multicomponent Peptide Stapling as a Diversity-Driven Tool for the Development of Inhibitors of Protein-Protein Interactions
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1RV1 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 295 | 0.1M TRIS pH 8, 0.2M Trimethyl N-oxide dihydrate, 20% PEG-2000 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.06 | 40.42 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 40.497 | α = 90 |
b = 40.497 | β = 90 |
c = 103.098 | γ = 120 |
Symmetry | |
---|---|
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 PILATUS 6M-F | 2018-04-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, DESY BEAMLINE P11 | 1.0332 | PETRA III, DESY | P11 |
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 | 2.09 | 35.07 | 99.9 | 0.07 | 0.072 | 0.017 | 0.999 | 27.2 | 17.1 | 6228 |
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 | 2.09 | 2.16 | 99.7 | 0.514 | 0.531 | 0.129 | 0.951 | 16.3 |
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 | 1RV1 | 2.09 | 35.07 | 5911 | 278 | 99.9 | 0.1981 | 0.1945 | 0.2715 | RANDOM | 32.701 |
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] | |
0.17 | 0.08 | 0.17 | -0.55 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 44.053 |
r_dihedral_angle_4_deg | 26.995 |
r_dihedral_angle_3_deg | 18.002 |
r_dihedral_angle_1_deg | 6.817 |
r_angle_refined_deg | 1.737 |
r_angle_other_deg | 0.984 |
r_chiral_restr | 0.093 |
r_bond_refined_d | 0.016 |
r_gen_planes_refined | 0.01 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 817 |
Nucleic Acid Atoms | |
Solvent Atoms | 51 |
Heterogen Atoms | 20 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
PHASER | phasing |