2V2J
Wild type recombinant horse spleen apoferritin cocrystallized with haemin in basic conditions
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2V2I | PDB ENTRY 2V2I |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 8.2 | RESERVOIR: CADMIUM SULFATE 0.04M, AMMONIUM SULFATE 0.5M, SODIUM AZIDE 0.003M DROP: 1UL PROTEIN AND 1 UL RESERVOIR, pH 8.2 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.2 | 61.5 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 182.981 | α = 90 |
| b = 182.981 | β = 90 |
| c = 182.981 | 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 | 100 | IMAGE PLATE | MARRESEARCH | MIRRORS | 2004-09-10 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU ULTRAX 18 | |||
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 | 2.22 | 29 | 98.3 | 0.04 | 25.7 | 4.2 | 13290 | ||||||||||||
| 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 | 2.22 | 2.3 | 97.8 | 0.14 | 9.3 | 3.8 | |||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2V2I | 2.22 | 105.41 | 12639 | 650 | 98.4 | 0.189 | 0.186 | 0.25 | RANDOM | 18.12 | ||||||
| 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 | 36.739 |
| r_dihedral_angle_4_deg | 20.658 |
| r_dihedral_angle_3_deg | 15.013 |
| r_dihedral_angle_1_deg | 5.745 |
| r_scangle_it | 4.282 |
| r_scbond_it | 3.09 |
| r_angle_refined_deg | 1.632 |
| r_mcangle_it | 1.557 |
| r_mcbond_it | 1.433 |
| r_angle_other_deg | 1.023 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1363 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 141 |
| Heterogen Atoms | 43 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
