6EZW
Crystal structure of a llama VHH antibody BCD090-M2 against human ErbB3 in space group C2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5IMK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293.15 | Reservoir solution: 0.1M MES-Imidazole pH 6.5, 0.02M Sodium formate, 0.02M Ammonium acetate, 0.02M Sodium citrate, 0.02M Sodium potassium tartrate, 0.02M Sodium oxamate, 20% v/v PEG 500MME, 10% w/v PEG 20 000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.13 | 42.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 65.759 | α = 90 |
b = 38.931 | β = 102.243 |
c = 47.482 | 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 | CCD | APEX II CCD | 2017-09-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | BRUKER IMUS MICROFOCUS | 1.54184 |
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 | 1.59842847381 | 33.2975053523 | 98.76472461 | 0.0731657786164 | 0.08065 | 0.0329161383793 | 0.998 | 12.7359219637 | 5.21442847012 | 15511 | 9.35381631249 |
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 | 1.59842847381 | 1.62598903761 | 0.386631506086 | 2.0696012381 | 2.29898648649 |
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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 5IMK | 1.59842847381 | 33.2975053523 | 15157 | 1517 | 96.5106653932 | 0.185278623977 | 0.182239424233 | 0.212561347445 | 14.3560089422 |
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 | 16.3181533076 |
f_angle_d | 0.822777572893 |
f_chiral_restr | 0.0564492238797 |
f_bond_d | 0.00590462819608 |
f_plane_restr | 0.00507859703921 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 981 |
Nucleic Acid Atoms | |
Solvent Atoms | 190 |
Heterogen Atoms |
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 |