4LAR
Crystal structure of a therapeutic single chain antibody in complex with amphetamine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3GK2 | PDB ENTRY 3GK2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.8 | 287.1 | 1.15M sodium citrate, 0.28M imidazole-malate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 287.1K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 42.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 34.545 | α = 90 |
b = 65.227 | β = 98.7 |
c = 48.593 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | MARMOSAIC 325 mm CCD | 2009-12-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | SSRL | BL9-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.38 | 50 | 93.3 | 0.093 | 0.04 | 24.9 | 4.4 | 7947 |
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 ENTRY 3GK2 | 2.38 | 48.03 | 7560 | 373 | 92.2 | 0.219 | 0.215 | 0.293 | RANDOM | 28.95 |
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] | |
2.89 | 0.24 | -2.06 | -0.76 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.288 |
r_dihedral_angle_4_deg | 20.575 |
r_dihedral_angle_3_deg | 19.789 |
r_dihedral_angle_1_deg | 7.111 |
r_scangle_it | 3.333 |
r_scbond_it | 2.186 |
r_angle_refined_deg | 1.865 |
r_mcangle_it | 1.588 |
r_mcbond_it | 0.851 |
r_chiral_restr | 0.109 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1778 |
Nucleic Acid Atoms | |
Solvent Atoms | 55 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CNS | refinement |
HKL-2000 | data collection |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
CNS | phasing |