X-ray Structure of a Second-Sphere H-bond Deletion Mutant of a De Novo Designed Self Assembled Peptide Tetramer Featuring a Cu(His)4(H2O) Coordination Motif
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 8VHS | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 295 | 0.1M Tris pH 8.5, 0.2M MgCl2.6H2O, 28% PEG 4000 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.95 | 37.05 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 34.553 | α = 90 |
| b = 45.309 | β = 98.54 |
| c = 40.524 | 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 EIGER X 16M | 2024-03-18 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | NSLS-II BEAMLINE 17-ID-2 | 0.97936 | NSLS-II | 17-ID-2 |
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 | 1.47 | 28.15 | 98.2 | 0.07 | 0.998 | 11.9 | 6.8 | 20743 | |||||||||||
| 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 | 1.47 | 1.51 | 0.49 | 0.97 | |||||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.47 | 28.15 | 19729 | 1009 | 98.18 | 0.2049 | 0.20337 | 0.2152 | 0.23624 | 0.245 | RANDOM | 31.232 | |||||
| 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] | |
| 0.02 | -0.03 | |||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_3_deg | 15.871 |
| r_long_range_B_other | 11.795 |
| r_long_range_B_refined | 11.719 |
| r_scangle_other | 7.006 |
| r_dihedral_angle_1_deg | 5.434 |
| r_mcangle_it | 5.205 |
| r_mcangle_other | 5.202 |
| r_scbond_it | 4.371 |
| r_scbond_other | 4.368 |
| r_mcbond_it | 3.537 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1130 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 93 |
| Heterogen Atoms | 1 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data scaling |
| XDS | data reduction |
| PHASER | phasing |
