Crystal structure of the 4CHRD domain of human chordin with Anderson-Evans polyoxotungstate
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 277.15 | 0.1M Morpheus buffer system 3 (Tris/Bicine) pH 8.0, 0.1M Morpheus amino acids (DL-Glutamic acid monohydrate, DL-Alanine, Glycine, DL-Serine and DL-Lysine monohydrochloride). Morpheus condition H11 with 1mM TEW and 0.05 mg/mL Trypsin |
| 2 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 277.15 | 0.1M Morpheus buffer system 3 (Tris/Bicine) pH 8.0, 0.1M Morpheus amino acids (DL-Glutamic acid monohydrate, DL-Alanine, Glycine, DL-Serine and DL-Lysine monohydrochloride). Morpheus condition H11 with 1mM TEW and 0.05 mg/mL Trypsin |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 91.302 | α = 90 |
| b = 91.302 | β = 90 |
| c = 323.657 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 2 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 99 | PIXEL | DECTRIS EIGER2 XE 16M | 2025-01-25 | M | SINGLE WAVELENGTH | ||||||
| 2 | 2 | 99 | PIXEL | DECTRIS EIGER2 XE 16M | 2025-01-25 | |||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9537 | Diamond | I04 |
| 2 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9537 | Diamond | I04 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 3.28 | 80.91 | 100 | 0.447 | 0.064 | 1 | 9.3 | 48.6 | 44114 | 124.45 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 3.28 | 3.54 | 100 | 1.367 | 0.522 | 1.1 | 38.9 | ||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3.28 | 79.52 | 1.33 | 39965 | 1944 | 99.76 | 0.2114 | 0.2096 | 0.2103 | 0.2469 | 0.2493 | 130.14 | |||||
| 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 | 5.007 |
| f_angle_d | 0.6194 |
| f_chiral_restr | 0.0427 |
| f_plane_restr | 0.0103 |
| f_bond_d | 0.0024 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6947 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 21 |
| Heterogen Atoms | 395 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| DIALS | data reduction |
| Aimless | data scaling |
| AutoSol | phasing |
| PHASER | phasing |
