2VXI
The binding of heme and zinc in Escherichia coli Bacterioferritin
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7.5 | 60% AMSO4, 20MM TRIS-HCL PH7.5, 0.1M NACL | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.93 | 57.74 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 208.1 | α = 90 |
| b = 208.1 | β = 90 |
| c = 142.768 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 42 21 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 | 2005-11-17 | M | MAD | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SRS BEAMLINE PX10.1 | 1.739, 1.729 | SRS | PX10.1 |
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 | 25 | 97.7 | 0.1 | 11 | 3.77 | 460546 | ||||||||||||
| 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 | 1.93 | 90.2 | 0.38 | 2.14 | 2.2 | |||||||||||||
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 | MAD | THROUGHOUT | NONE | 1.91 | 147.44 | 231295 | 4739 | 98.68 | 0.17925 | 0.17851 | 0.21561 | RANDOM | 24.852 | ||||||
| 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] | |
| 0.03 | 0.03 | -0.07 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 38.97 |
| r_dihedral_angle_4_deg | 23.443 |
| r_dihedral_angle_3_deg | 13.743 |
| r_scangle_it | 9.676 |
| r_scbond_it | 6.573 |
| r_dihedral_angle_1_deg | 4.722 |
| r_mcangle_it | 4.184 |
| r_mcbond_it | 2.558 |
| r_angle_refined_deg | 1.704 |
| r_chiral_restr | 0.118 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 15528 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 2208 |
| Heterogen Atoms | 685 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | model building |
| SCALEPACK | data scaling |
| SHELXD | phasing |
| MLPHARE | phasing |
| DM | phasing |
| REFMAC | phasing |
| REFMAC | refinement |
