6IRI
Crystal structure of the minor ferredoxin from Thermosynechococcus elongatus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5AUI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 100 mM HEPES (pH 7.5), 2.4 M ammonium sulfate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.72 | 28.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 27.946 | α = 90 |
b = 51.121 | β = 116.15 |
c = 31.57 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 100 | CCD | ADSC QUANTUM 315 | 2018-01-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL38B1 | 1.0 | SPring-8 | BL38B1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 1.38 | 28.34 | 99.3 | 0.056 | 0.999 | 12.82 | 3.68 | 16325 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.38 | 1.47 | 98.9 | 0.585 | 0.718 | 2 | 3.62 |
Refinement
Statistics | |||||||||||||||||||
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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 | 5AUI | 1.38 | 28.34 | 15531 | 793 | 99.7 | 0.1146 | 0.1124 | 0.157 | RANDOM | 18.168 |
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] | |
-0.03 | -0.32 | 1.18 | -0.57 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 39.356 |
r_dihedral_angle_2_deg | 37.032 |
r_dihedral_angle_3_deg | 12.446 |
r_sphericity_bonded | 10.86 |
r_dihedral_angle_4_deg | 10.182 |
r_rigid_bond_restr | 9.159 |
r_dihedral_angle_1_deg | 6.448 |
r_angle_refined_deg | 2.086 |
r_angle_other_deg | 1.154 |
r_chiral_restr | 0.132 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 821 |
Nucleic Acid Atoms | |
Solvent Atoms | 114 |
Heterogen Atoms | 9 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |
PDB_EXTRACT | data extraction |