4GQP
Structure based design of sub-nanomolar affinity anti-methamphetamine single chain antibodies.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3GKZ | PDB ENTRY 3GKZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.25 | 287.15 | 0.917 M sodium citrate, pH 8.2, 0.324 M imidazole-malate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 287.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.02 | 39 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 34.516 | ¦Á = 90 |
b = 65.265 | ¦Â = 98.2 |
c = 48.483 | ¦Ã = 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 | Rh coated flat mirrors | 2012-04-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.97946 | SSRL | BL9-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 50 | 99.2 | 0.087 | 34.2 | 4.8 | 14299 | 14299 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2 | 2.03 | 100 | 0.33 | 8.1 | 5.1 |
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 3GKZ | 2 | 38.66 | 13554 | 719 | 99.03 | 0.19669 | 0.19369 | 0.25361 | RANDOM | 27.454 |
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] | |
0.06 | -0.01 | -0.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.737 |
r_dihedral_angle_4_deg | 21.744 |
r_dihedral_angle_3_deg | 16.957 |
r_dihedral_angle_1_deg | 7.461 |
r_scangle_it | 4.36 |
r_scbond_it | 3.148 |
r_mcangle_it | 2.039 |
r_angle_refined_deg | 1.987 |
r_mcbond_it | 1.21 |
r_chiral_restr | 0.135 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1756 |
Nucleic Acid Atoms | |
Solvent Atoms | 79 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
CCP4 | model building |
REFMAC | refinement |
Coot | model building |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CCP4 | phasing |