2J5L
Structure of a Plasmodium falciparum apical membrane antigen 1-Fab F8. 12.19 complex
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 4.6 | 290 | CRYSTALLISATION TRIALS WERE CARRIED OUT WITH PFAMA1 ECTOPLASMIC CONSTRUCTION CORRESPONDING TO DOMAINS II-III. THE FAB FRAGMENT WAS INCUBATED IN SMALL STOICHIOMETRIC EXCESS WITH THE RECOMBINANT PROTEIN (1.2:1) BEFORE ADDING CRYSTALLISATION BUFFERS. CRYSTALLISATION DROPS WERE PREPARED BY MIXING 0.8 MICROL OF PROTEIN WITH 0.8 MICROL OF RESERVOIR BUFFER COMPRISING 12% PEG 6000 AND 0.1 M SODIUM ACETATE AT PH 4.6. THE FINAL PROTEIN CONCENTRATION WAS 3.2 MG/ML. CRYSTALS APPEARED AFTER 5 DAYS AT 17 DEGREE C. | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.2 | 45 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 171.9 | α = 90 |
| b = 171.9 | β = 90 |
| c = 44.2 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 63 |
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 | ADSC CCD | M | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 | |
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 | 2.8 | 20 | 96 | 0.25 | 12.1 | 21.2 | 18102 | -3 | |||||||||||
| 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 | 2.8 | 3 | 80.4 | 1.16 | 2.7 | 16.2 | |||||||||||||
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2J4W | 2.9 | 20 | 16037 | 847 | 99.8 | 0.215 | 0.212 | 0.278 | RANDOM | 61.04 | ||||||
| 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] | |
| -6.02 | -3.01 | -6.02 | 9.02 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.189 |
| r_dihedral_angle_4_deg | 25.941 |
| r_dihedral_angle_3_deg | 25.326 |
| r_dihedral_angle_1_deg | 9.908 |
| r_scangle_it | 3.714 |
| r_mcangle_it | 3.059 |
| r_scbond_it | 2.614 |
| r_angle_refined_deg | 2.386 |
| r_mcbond_it | 1.745 |
| r_symmetry_hbond_refined | 0.34 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3605 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| AMoRE | phasing |
