Crystal Structure of Silicatein Alpha from Marine Sponge Tethya aurantium
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 2VHS | pdbid 2VHS |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | IN CELL | | 298 | in vivo |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.56 | 51.95 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 59.6 | α = 90 |
| b = 59.6 | β = 90 |
| c = 116.29 | 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 EIGER X 16M | | 2019-04-21 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.0 | SLS | X06SA |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.4 | 51.5 | 100 | 0.91 | 6.1 | 159 | | 9827 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 2.4 | 2.486 | | | 0.58 | | | |
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) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdbid 2VHS | 2.4 | 47.18 | 9337 | 492 | 99.87 | 0.2436 | 0.2403 | 0.25 | 0.302 | 0.3 | RANDOM | 49.104 |
| 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] |
|---|
| 1.46 | 0.73 | | 1.46 | | -4.74 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_2_deg | 33.152 |
| r_dihedral_angle_4_deg | 17.532 |
| r_dihedral_angle_3_deg | 17.051 |
| r_dihedral_angle_1_deg | 6.237 |
| r_angle_refined_deg | 1.367 |
| r_angle_other_deg | 0.79 |
| r_chiral_restr | 0.073 |
| r_bond_refined_d | 0.011 |
| r_gen_planes_refined | 0.005 |
| r_bond_other_d | 0.001 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_2_deg | 33.152 |
| r_dihedral_angle_4_deg | 17.532 |
| r_dihedral_angle_3_deg | 17.051 |
| r_dihedral_angle_1_deg | 6.237 |
| r_angle_refined_deg | 1.367 |
| r_angle_other_deg | 0.79 |
| r_chiral_restr | 0.073 |
| r_bond_refined_d | 0.011 |
| r_gen_planes_refined | 0.005 |
| r_bond_other_d | 0.001 |
| r_gen_planes_other | 0.001 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1586 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 24 |
| Heterogen Atoms | |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
| MOLREP | phasing |
