1JZL
Crystal structure of Sapharca inaequivalvis HbI, I114M mutant ligated to carbon monoxide.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3SDH |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 7.5 | 296 | 2.1-2.3M Phosphate buffer, pH 7.5, Microbatch, temperature 296K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.26 | 45.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 93.11 | α = 90 |
b = 43.97 | β = 122.01 |
c = 83.44 | 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 | 296 | IMAGE PLATE | RIGAKU RAXIS IIC | yale mirrors | 2000-02-14 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 296 | IMAGE PLATE | RIGAKU RAXIS IIC | yale mirrors | 2000-02-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 | ||
2 | ROTATING ANODE | RIGAKU RU200 | 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 | ||||||||
1,2 | 1.5 | 40 | 88.1 | 0.066 | 12.6 | 3 | 46282 | 40783 | 1 | 1 | 20.4 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
1.5 | 1.55 | 39.9 | 0.235 | 1842 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3SDH | 1.5 | 28.62 | 40765 | 40765 | 4098 | 88.3 | 0.217 | 0.215 | 0.215 | 0.236 | RANDOM | 17.9 |
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] | |
0.65 | -0.09 | 1.5 | -2.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 19 |
c_improper_angle_d | 1.12 |
c_mcangle_it | 1.12 |
c_angle_deg | 1.1 |
c_mcbond_it | 0.72 |
c_scangle_it | 0.22 |
c_scbond_it | 0.13 |
c_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2240 |
Nucleic Acid Atoms | |
Solvent Atoms | 165 |
Heterogen Atoms | 90 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |