3D7O
Human hemoglobin, nitrogen dioxide anion modified
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1IRD | PDB Entry 1IRD |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LIQUID DIFFUSION | 6.8 | 295 | Sodium phosphate, Potassium phosphate, Toluene, Hemoglobin, pH 6.8, LIQUID DIFFUSION, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.21 | 44.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.538 | α = 90 |
b = 53.538 | β = 90 |
c = 191.77 | 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 | 100 | IMAGE PLATE | RIGAKU RAXIS IV | Osmic | 2008-05-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R | 1.5418 |
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 | 1.8 | 16.37 | 99.8 | 0.082 | 10.2 | 7.74 | 26808 | 26808 | 2 | 2 | 36.6 |
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) | |||||||||||
1.8 | 1.86 | 98.3 | 0.457 | 2.9 | 4.2 | 2558 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB Entry 1IRD | 1.8 | 16.37 | 2 | 2 | 26805 | 26803 | 1347 | 99.55 | 0.237 | 0.208 | 0.206 | 0.237 | RANDOM | 28.993 |
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] | |
-0.05 | -0.05 | 0.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.389 |
r_dihedral_angle_3_deg | 14.986 |
r_dihedral_angle_4_deg | 12.709 |
r_dihedral_angle_1_deg | 5.193 |
r_scangle_it | 3.477 |
r_scbond_it | 2.384 |
r_mcangle_it | 1.551 |
r_angle_refined_deg | 1.522 |
r_mcbond_it | 1.011 |
r_symmetry_vdw_refined | 0.306 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2217 |
Nucleic Acid Atoms | |
Solvent Atoms | 152 |
Heterogen Atoms | 99 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrystalClear | data collection |
d*TREK | data reduction |