2YK1
Structure of human anti-nicotine Fab fragment in complex with nicotine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BOS | PDB ENTRY 2BOS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | SITTING DROP, 5% PEG 3000, 0.1 M MES PH 6.0, 30% (V/V) PEG 200, 10 MG/ML PROTEIN, 20 MM NICOTINE. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 41 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 76.11 | ¦Á = 90 |
b = 78.87 | ¦Â = 116.55 |
c = 75.47 | ¦Ã = 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 | ADSC QUANTUM 210 | SAGITALLY FOCUSING GE(220) AND A MULTILAYER | 2008-10-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | ESRF | ID14-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.85 | 30 | 95 | 0.04 | 8.4 | 2.1 | 34228 | 1.8 | 22 |
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 | 1.85 | 1.95 | 91.5 | 0.22 | 1.8 | 2.1 |
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 2BOS | 1.85 | 27.35 | 30695 | 1635 | 94.59 | 0.22648 | 0.22446 | 0.26434 | RANDOM | 28.267 |
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] | |
0.02 | -0.11 | -0.47 | 0.36 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.437 |
r_dihedral_angle_4_deg | 20.866 |
r_dihedral_angle_3_deg | 12.542 |
r_dihedral_angle_1_deg | 6.174 |
r_scangle_it | 2.142 |
r_scbond_it | 1.421 |
r_angle_refined_deg | 1.199 |
r_mcangle_it | 1.049 |
r_mcbond_it | 0.57 |
r_chiral_restr | 0.081 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2756 |
Nucleic Acid Atoms | |
Solvent Atoms | 244 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |