2V2L
Mutant (E53,56,57,60Q) recombinant horse spleen apoferritin cocrystallized with haemin in acidic 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 | 5.5 | RESERVOIR: CADMIUM SULFATE 0.13M, AMMONIUM SULFATE 0.8M, SODIUM ACETATE 0.1M PH 5.5, SODIUM AZIDE 0.003M. DROP: 2 UL PROTEIN AND 2 UL RESERVOIR | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.2 | 61.2 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 182.455 | α = 90 |
| b = 182.455 | β = 90 |
| c = 182.455 | 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 | CCD | MARRESEARCH | TWO MIRRORS ARE USED FOR VERTICAL FOCUSSING. | 2003-11-14 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE BM30A | ESRF | BM30A | |
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 | 1.9 | 20 | 100 | 0.06 | 37.1 | 10.5 | 21041 | ||||||||||||
| 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 | 1.9 | 1.94 | 99.9 | 0.49 | 5.3 | 7 | |||||||||||||
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 | 1.9 | 105.41 | 19645 | 1064 | 98.2 | 0.19 | 0.188 | 0.216 | RANDOM | 19.95 | ||||||
| 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 | 37.377 |
| r_dihedral_angle_4_deg | 19.804 |
| r_dihedral_angle_3_deg | 13.44 |
| r_dihedral_angle_1_deg | 5.435 |
| r_scangle_it | 4.763 |
| r_scbond_it | 3.459 |
| r_mcangle_it | 1.758 |
| r_mcbond_it | 1.664 |
| r_angle_refined_deg | 1.556 |
| r_angle_other_deg | 0.991 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1372 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 174 |
| Heterogen Atoms | 18 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
