3WCU
The structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: Deoxygenated form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3WCT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 13-18% PEG 3350, 0-5mM Ca acetate/Mg acetate, 100mM HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.57 | 52.06 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 108.872 | α = 90 |
b = 108.872 | β = 90 |
c = 195.157 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 | Bruker DIP-6040 | 2009-07-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 0.9000 | SPring-8 | BL44XU |
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 | 2.9 | 50 | 96.5 | 0.096 | 13.2 | 5.7 | 28054 | 28054 | -3 | 95.4 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.9 | 3 | 98.8 | 0.503 | 4.2 | 5.6 | 2864 |
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 | FOURIER SYNTHESIS | THROUGHOUT | 3WCT | 2.9 | 42.45 | 27985 | 1436 | 96.5 | 0.246 | 0.246 | 0.292 | RANDOM | 70.7541 |
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] | |
-5.25 | -5.25 | 10.51 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 19.1 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.81 |
c_bond_d | 0.009 |
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 | 9138 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 488 |
Software
Software | |
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Software Name | Purpose |
BSS | data collection |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |