Crystal structure of ferritin mutantFr-H8 (R52H/E53H/E56H/E57H/R59H/E60H/E63H/R64H)
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1DAT | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | Precipitant: (NH4)2SO4 (0.5-1.0M), CdSO4(12-20mM) Protein: 15-20mg/ml Crystallization drop: 1:1 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.16 | 61.1 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 181.999 | α = 90 |
| b = 181.999 | β = 90 |
| c = 181.999 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | F 4 3 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 93 | PIXEL | RIGAKU HyPix-6000HE | 2024-04-08 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU FR-E DW | 1.543 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.5 | 22.26 | 99.5 | 0.093 | 0.099 | 0.032 | 0.997 | 17.3 | 9.4 | 41576 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 1.5 | 1.6 | 100 | 0.881 | 0.96 | 0.376 | 0.797 | 2.1 | 6.8 | ||||||||||
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 (All) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.5 | 22.235 | 41384 | 2089 | 99.107 | 0.217 | 0.2158 | 0.2249 | 0.2424 | 0.2484 | 13.528 | ||||||
| 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 |
| r_dihedral_angle_2_deg | 37.843 |
| r_dihedral_angle_4_deg | 19.426 |
| r_dihedral_angle_3_deg | 13.138 |
| r_lrange_it | 5.851 |
| r_lrange_other | 5.616 |
| r_dihedral_angle_1_deg | 4.764 |
| r_scangle_it | 4.09 |
| r_scangle_other | 3.863 |
| r_scbond_it | 2.578 |
| r_scbond_other | 2.42 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1391 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 260 |
| Heterogen Atoms | 23 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CrysalisPro | data collection |
| CrysalisPro | data reduction |
| Aimless | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
| Coot | model building |
