2WLB
Adrenodoxin-like ferredoxin Etp1fd(516-618) of Schizosaccharomyces pombe mitochondria
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1E6E | PDB ENTRIES 1E6E,1AYF,1L6V,2BT6 |
experimental model | PDB | 1AYF | PDB ENTRIES 1E6E,1AYF,1L6V,2BT6 |
experimental model | PDB | 1L6V | PDB ENTRIES 1E6E,1AYF,1L6V,2BT6 |
experimental model | PDB | 2BT6 | PDB ENTRIES 1E6E,1AYF,1L6V,2BT6 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.4 | 277 | VAPOUR DIFFUSION, SITTING DROP, 4 DEGR. CENTIGRADE. RESERVOIR: 0.04M HEPES,1.8M NA-CITRATE, 3% GLYCEROL,PH7.0. PROTEIN SOLUTION: 18.4MG/ML PROTEIN, 20MM POTASSIUMPHOSPHATE,PH7.4. 0.3 PLUS 0.3 MICROLITER DROPLET. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.83 | 56.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.965 | α = 90 |
b = 81.965 | β = 90 |
c = 68.289 | γ = 120 |
Symmetry | |
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Space Group | P 32 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 | 278 | IMAGE PLATE | MAR scanner 345 mm plate | 2004-04-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU H2B |
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 | 2.6 | 20 | 99.5 | 0.11 | 8.5 | 3.4 | 8006 | 56.1 |
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 | 2.6 | 2.78 | 92.4 | 0.51 | 3.4 | 3.5 |
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRIES 1E6E,1AYF,1L6V,2BT6 | 2.6 | 20 | 8006 | 390 | 99.5 | 0.184 | 0.182 | 0.235 | RANDOM | 45.15 |
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] | |
0.31 | 0.16 | 0.31 | -0.47 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.132 |
r_dihedral_angle_3_deg | 18.903 |
r_dihedral_angle_4_deg | 13.795 |
r_scangle_it | 9.292 |
r_scbond_it | 6.76 |
r_dihedral_angle_1_deg | 5.593 |
r_mcangle_it | 3.93 |
r_mcbond_it | 3.23 |
r_angle_refined_deg | 1.453 |
r_angle_other_deg | 0.915 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1567 |
Nucleic Acid Atoms | |
Solvent Atoms | 2 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
SWISS-MODELLER | phasing |
PHASER | phasing |
REFMAC | refinement |