6F0D
Crystal structure of a llama VHH antibody BCD090-M2 against human ErbB3 in space group P1 with cadmium ions
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293.15 | Protein solution: 17 mg/ml in 20 mM HEPES pH 7.5, 50 mM NaCl Reservoir solution: 0.1 M MES pH 6.5, 12% w/v PEG 3350, 5 mM CdSO4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.21 | 44.39 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 35.766 | α = 89.992 |
b = 41.526 | β = 67.921 |
c = 46.487 | γ = 76.062 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 293.15 | CCD | APEX II CCD | 2017-10-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | BRUKER IMUS MICROFOCUS | 1.54184 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.90000753152 | 32.3416437838 | 100 | 0.144282201545 | 0.15 | 0.0395 | 0.997 | 12.9301230207 | 13.0920515404 | 18859 | 15.2376005709 |
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 | 1.90000753152 | 1.93276488574 | 0.833387206263 | 1.56474169635 | 4.79135135135 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 6EZW | 1.90000753152 | 32.3416437838 | 0.119369942261 | 18248 | 1829 | 96.765298547 | 0.178155788177 | 0.17376345673 | 0.217608275476 | 19.8620885272 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 20.0180771652 |
f_angle_d | 1.53085536185 |
f_chiral_restr | 0.072200302117 |
f_bond_d | 0.0139147074203 |
f_plane_restr | 0.0082941237946 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1962 |
Nucleic Acid Atoms | |
Solvent Atoms | 155 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
APEX 2 | data collection |
SAINT | data reduction |
SADABS | data scaling |
PHASER | phasing |
PHENIX | model building |
Coot | model building |
PHENIX | refinement |