3NG6
The crystal structure of hemoglobin I from Trematomus newnesi in deoxygenated state obtained through an oxidation/reduction cycle in which potassium hexacyanoferrate and sodium dithionite were alternatively added
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2H8F | PDB entry 2H8F |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | LIQUID DIFFUSION | 6 | 293 | protein at 10 mg/ml, in a 100 mM sodium acetate buffer pH 6.0, 2mM dithionite, poured into a capillary containing 20% (w/v) MPEG 5000 (2 mM dithionite), LIQUID DIFFUSION, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.8 | 56.06 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.882 | α = 90 |
b = 61.882 | β = 90 |
c = 187.014 | γ = 90 |
Symmetry | |
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Space Group | P 41 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ENRAF-NONIUS | mirrors | 2010-01-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.2 | 26.6 | 32263 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 2H8F | 2.2 | 26.6 | 32075 | 1607 | 90.9 | 0.195 | 0.247 | RANDOM |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
s_bond_d | |
s_angle_d | |
s_similar_dist | |
s_from_restr_planes | |
s_zero_chiral_vol | |
s_non_zero_chiral_vol | |
s_anti_bump_dis_restr | |
s_rigid_bond_adp_cmpnt | |
s_similar_adp_cmpnt | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4494 |
Nucleic Acid Atoms | |
Solvent Atoms | 105 |
Heterogen Atoms | 172 |
Software
Software | |
---|---|
Software Name | Purpose |
CrystalClear | data collection |
AMoRE | phasing |
SHELXL-97 | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |