6FDR
7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT 100K, NA DITHIONITE REDUCED AT PH 8.5, RESOLUTION 1.4 A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6FD1 | PDB ENTRY 6FD1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.8 | PROTEIN CRYSTALLIZED FROM 60% SAT. AMMONIUM SULFATE, 0.4M TRIS-HCL, PH 7.8. CRYSTALS WERE SOAKED IN 5MM NA DITHIONITE, 0.15M TRIS/HCL PH 8.5 BEFORE DATA COLLECTION |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.91 | 57.73 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.74 | α = 90 |
b = 54.74 | β = 90 |
c = 93.77 | 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 | AREA DETECTOR | SIEMENS HI-STAR | 1998-09-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | MACSCIENCE |
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 | 1.4 | 100 | 82.8 | 0.15 | 13.6 | 4.56 | 24027 |
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) | |||||||||||
1.4 | 1.5 | 55.3 | 0.44 | 0.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | OTHER | PDB ENTRY 6FD1 | 1.4 | 100 | 22762 | 82.8 | 0.175 |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
1 | 776 | 1000 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_from_restr_planes | 0.379 |
s_approx_iso_adps | 0.133 |
s_zero_chiral_vol | 0.122 |
s_non_zero_chiral_vol | 0.118 |
s_similar_adp_cmpnt | 0.106 |
s_angle_d | 0.025 |
s_rigid_bond_adp_cmpnt | 0.014 |
s_anti_bump_dis_restr | 0.012 |
s_bond_d | 0.008 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1617 |
Nucleic Acid Atoms | |
Solvent Atoms | 145 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
TRIVIAL | model building |
SHELXL | refinement |
X-GEN | data reduction |
X-GEN | data scaling |
TRIVIAL | phasing |