2Y36
Crystal structure analysis of the anti-(4-hydroxy-3-nitrophenyl)- acetyl murine germline antibody BBE6.12H3 Fab fragment in complex with a phage display derived dodecapeptide DLWTTAIPTIPS
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.1 | 0.05M TRIS HCL, 0.025% SODIUM AZIDE, PEG 3350., pH 7.1 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.02 | 39.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.01 | α = 90 |
b = 63.62 | β = 90.4 |
c = 113.38 | 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 | 287 | CCD | MARMOSAIC 225 mm CCD | BENT COLLIMATING MIRROR AND TOROID | 2009-08-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | ESRF | BM14 |
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 | 2.7 | 50 | 100 | 0.07 | 11.3 | 5.1 | 11098 | 28.3 |
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 | 2.7 | 8.5 | 100 | 0.28 | 4.1 | 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 | NATIVE FAB | 2.7 | 50 | 9995 | 1081 | 90.1 | 0.2305 | 0.2305 | 0.2477 | RANDOM | 42.4 |
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] | |
-12.165 | -1.132 | 26.388 | -14.223 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 28.5 |
c_angle_deg | 1.96434 |
c_improper_angle_d | 1.3 |
c_bond_d | 0.009918 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d | |
c_angle_d_na | |
c_angle_d_prot | |
c_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3294 |
Nucleic Acid Atoms | |
Solvent Atoms | 99 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |