1UWG
Molecular Mechanism of Enantioselective Proton Transfer to Carbon in Catalytic Antibody 14D9
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1D5I | PDB ENTRY 1D5I |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8.5 | 45% MPD, 0.1 M TRIS, PH 8.5, 0.2 M AMMONIUM DIHYDROGEN PHOSPHATE,0.1M NAI |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.48 | 50.48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.47 | α = 90 |
b = 97.92 | β = 99.28 |
c = 70.88 | 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 | 110 | IMAGE PLATE | RIGAKU RAXIS IV | CONFOCAL MIRRORS | 2001-03-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU300 |
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 | 2.79 | 20 | 99.4 | 0.133 | 0.375 | 3.7 | 22991 |
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 | 2.79 | 2.85 | 85.8 | 0.42 | 3.2 | 3.6 |
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 1D5I | 2.79 | 20 | 21887 | 1011 | 100 | 0.207 | 0.204 | 0.276 | RANDOM | 7.94 |
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] | |
0.17 | -0.74 | -1.11 | 0.7 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 4.021 |
r_scangle_it | 3.414 |
r_scbond_it | 2.11 |
r_angle_refined_deg | 1.259 |
r_mcangle_it | 1.118 |
r_symmetry_hbond_refined | 0.8 |
r_mcbond_it | 0.646 |
r_symmetry_vdw_refined | 0.508 |
r_nbd_refined | 0.285 |
r_xyhbond_nbd_refined | 0.22 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6344 |
Nucleic Acid Atoms | |
Solvent Atoms | 85 |
Heterogen Atoms | 70 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |