1SN2
Crystal Structure of Sea Bream Transthyretin at 1.90A Resolution
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1F41 | Human transthyretin, pdb code 1F41 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5 | 296 | PEG 1550 MME, sodium citrate, ammonium sulphate, nickel sulphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.14 | 42.64 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 58.497 | ¦Á = 90 |
| b = 58.497 | ¦Â = 90 |
| c = 140.71 | ¦Ã = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | M | SINGLE WAVELENGTH | |||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X11 | EMBL/DESY, HAMBURG | X11 | |
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 | 1.75 | 50 | 97.1 | 0.047 | 46104 | ||||||||||||||
| 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 | 1.75 | 1.81 | 92.2 | 0.451 | |||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | Human transthyretin, pdb code 1F41 | 1.75 | 19.84 | 46104 | 39742 | 4439 | 100 | 0.1783 | 0.17836 | 0.17489 | 0.20964 | RANDOM | 21.58 | ||||
| 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] | |
| -0.18 | -0.18 | 0.36 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_3_deg | 18.389 |
| r_dihedral_angle_1_deg | 3.959 |
| r_scangle_it | 2.757 |
| r_scbond_it | 1.622 |
| r_mcangle_it | 1.316 |
| r_angle_refined_deg | 1.303 |
| r_angle_other_deg | 0.718 |
| r_mcbond_it | 0.695 |
| r_symmetry_vdw_refined | 0.326 |
| r_symmetry_vdw_other | 0.278 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3529 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 361 |
| Heterogen Atoms | 5 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| CNS | phasing |
