3WAB
Carboxypeptidase B in complex with DD2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ZG7 | PDB ENTRY 1ZG7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 296 | 100mM sodium cacodylate (pH 5.3-6.8), 100mM zinc acetate, 5-15% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.84 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.314 | α = 90 |
b = 79.314 | β = 90 |
c = 100.342 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | 86 | IMAGE PLATE | RIGAKU RAXIS II | 2009-11-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.541865 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.15 | 15 | 99.5 | 17871 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.15 | 2.23 | 99.9 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1ZG7 | 2.154 | 15 | 17868 | 1786 | 100 | 0.2067 | 0.2777 | RANDOM | 18.2892 |
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] | |
2.319 | 2.319 | -4.638 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_scangle_it | 2.289 |
c_scbond_it | 1.728 |
c_mcangle_it | 1.545 |
c_mcbond_it | 1.076 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2436 |
Nucleic Acid Atoms | |
Solvent Atoms | 223 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data reduction |
CNS | refinement |
PDB_EXTRACT | data extraction |
RAPID-AUTO | data collection |
RAPID-AUTO | data reduction |
d*TREK | data scaling |
CNS | phasing |