4ODC
Crystal structure of Trematomus bernacchii hemoglobin in a partially cyanided state
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2PEG | pdb entry 2peg |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LIQUID DIFFUSION | 7.6 | 293 | Crystallization of partially cyanided HbTb (CN-HbTb) was carried out at pH 7.6 and room temperature via liquid-diffusion technique, using a capillary. Precipitant solution: 10% (w/v) PEG MME 5000, 50 mM TRIS-HCl pH 7.6, LIQUID DIFFUSION, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.27 | 62.33 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 86.88 | α = 90 |
b = 87.88 | β = 99.66 |
c = 55.25 | 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 | 100 | CCD | MAR CCD 165 mm | 2003-05-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 5.2R | 1.0 | ELETTRA | 5.2R |
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 | 1.54 | 30 | 98.8 | 0.042 | 5 | 61743 | 61743 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | FOURIER SYNTHESIS | THROUGHOUT | pdb entry 2peg | 1.54 | 30 | 61743 | 61743 | 3115 | 0.165 | 0.165 | 0.197 | RANDOM |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2242 |
Nucleic Acid Atoms | |
Solvent Atoms | 405 |
Heterogen Atoms | 96 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
SHELXS | phasing |
SHELXL-97 | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |