7RLY
Antibody 2F2 in complex with P. vivax CSP peptide DRAAGQPAGDRADGQPA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1XIW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 295 | 0.1M sodium citrate pH 5.0 and PEG 6000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.66 | 53.79 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 71.723 | α = 95.263 |
b = 82.287 | β = 113.784 |
c = 82.747 | γ = 111.471 |
Symmetry | |
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Space Group | P 1 |
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 | 80 | PIXEL | DECTRIS PILATUS 6M | 2020-02-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 1.033167 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | 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 | 2.67 | 29.61 | 98.3 | 0.987 | 4.7 | 3.6 | 43179 | 46.97 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.67 | 2.77 | 97.8 | 0.669 | 1.5 | 3.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1xiw | 2.67 | 29.61 | 1.97 | 43161 | 2162 | 98.32 | 0.1875 | 0.1854 | 0.2272 | 51 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 9.623 |
f_angle_d | 0.5698 |
f_chiral_restr | 0.0437 |
f_plane_restr | 0.0046 |
f_bond_d | 0.0023 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10338 |
Nucleic Acid Atoms | |
Solvent Atoms | 160 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |