8TFE
Crystal structure of Fab fragment of anti-HCV E2 antibody (CBH-7)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6X9X |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 295 | 0.1M Sodium phosphate dibasic pH 4.2, 0.2 M NaCl, and 20% PEG8000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.94 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.935 | α = 90 |
b = 101.912 | β = 100.24 |
c = 109.936 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 100 | PIXEL | DECTRIS EIGER X 16M | 2021-10-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 0.979 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.62 | 50 | 98.4 | 0.09 | 0.098 | 0.038 | 0.981 | 27.75 | 6.4 | 107383 | 19.42 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.62 | 1.65 | 98.5 | 0.544 | 0.595 | 0.238 | 0.911 | 5.6 |
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 | 6X9X | 1.62 | 46.14 | 102019 | 5362 | 98.13 | 0.17881 | 0.17695 | 0.21384 | RANDOM | 23.222 |
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] | |
2.84 | -0.37 | -1.2 | -1.41 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.106 |
r_dihedral_angle_4_deg | 20.794 |
r_dihedral_angle_3_deg | 13.626 |
r_dihedral_angle_1_deg | 7.315 |
r_long_range_B_refined | 6.071 |
r_long_range_B_other | 6.071 |
r_scangle_other | 4.463 |
r_scbond_other | 3.021 |
r_scbond_it | 3.02 |
r_mcangle_other | 2.933 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6449 |
Nucleic Acid Atoms | |
Solvent Atoms | 782 |
Heterogen Atoms | 29 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
SCALA | data scaling |
PHASER | phasing |