2J4W
Structure of a Plasmodium vivax apical membrane antigen 1-Fab F8.12.19 complex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.4 | PVAMA1 AND FAB-F8.12.19 WERE MIXED IN A 1:1 STOICHIOMETRIC RATIO AND LEFT TO INCUBATE FOR 4 HOURS AT ROOM TEMPERATURE TO FORM THE ANTIBODY-ANTIGEN COMPLEX BEFORE MIXING WITH CRYSTALLISATION SCREENING BUFFERS. CRYSTALS USED FOR DIFFRACTION MEASUREMENTS WERE OBTAINED AS FOLLOWS. THE CRYSTALLISATION BUFFER IN THE RESERVOIR COMPRISED 10% PEG 6000 AND 0.1 M SODIUM ACETATE BUFFERED TO PH 4.4. THE CRYSTALLISATION DROP WAS PREPARED BY ADDING 0.8 MICROLITRES OF THE CRYSTALLISATION BUFFER TO 0.8 MICROLITRES OF THE PVAMA1-FAB COMPLEX, GIVING A FINAL PROTEIN CONCENTRATION OF 3.9 MG/ML. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.61 | 65.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 171.787 | α = 90 |
b = 171.787 | β = 90 |
c = 44.748 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.5 | 20 | 98.1 | 0.14 | 14.8 | 10 | 26533 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.5 | 2.6 | 88 | 0.93 |
Refinement
Statistics | |||||||||||||||||||
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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 ENTRIES 2IGF, 1W8K | 2.5 | 20 | 24858 | 1335 | 98.7 | 0.19 | 0.187 | 0.241 | RANDOM | 42.31 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-2.57 | -1.28 | -2.57 | 3.85 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.558 |
r_dihedral_angle_4_deg | 23.852 |
r_dihedral_angle_3_deg | 20.325 |
r_dihedral_angle_1_deg | 7.416 |
r_scangle_it | 3.508 |
r_mcangle_it | 2.622 |
r_scbond_it | 2.547 |
r_angle_refined_deg | 1.893 |
r_mcbond_it | 1.504 |
r_nbtor_refined | 0.315 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3606 |
Nucleic Acid Atoms | |
Solvent Atoms | 155 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
AMoRE | phasing |