Crystal Structure of YAP1 and Dendrin complex 2
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 6JK0 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 289 | 28-35% w/v pentaerythritol propoxylat 426 (5/4 PO/OH), 100mM HEPES (pH 7.5) |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 3.42 | 64.06 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 77.376 | α = 90 |
| b = 77.376 | β = 90 |
| c = 116.763 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 41 21 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 | | 2018-01-14 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | SSRF BEAMLINE BL19U1 | 0.97855 | SSRF | BL19U1 |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | fixed target |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 50 | 100 | 0.079 | 32.8 | 12.8 | | 24702 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 2 | 2.03 | 100 | | 0.698 | 3.7 | 11.2 | |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6JK0 | 2 | 29.191 | 23948 | 1941 | 97.21 | 0.1874 | 0.1853 | 0.19 | 0.2111 | 0.21 | |
| 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 | 14.548 |
| f_angle_d | 1.103 |
| f_chiral_restr | 0.043 |
| f_bond_d | 0.007 |
| f_plane_restr | 0.005 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1433 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 198 |
| Heterogen Atoms | |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| PHASER | phasing |
