4WBJ
Crystal structure of Bradyrhizobium japonicum ScoI in the oxidized state
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4TXO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 292 | 0.1M SPG, 25% PEG15000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 41.38 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.776 | α = 90 |
b = 82.629 | β = 90.03 |
c = 45.853 | 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 | 80 | PIXEL | DECTRIS PILATUS 6M | 2014-08-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.3 | 45.8 | 91.9 | 0.039 | 0.042 | 28.35 | 7 | 65098 | -3 | 15.447 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.3 | 1.33 | 83.6 | 0.151 | 0.163 | 9.94 |
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 | 4txo | 1.3 | 45.8 | 65098 | 3255 | 91.86 | 0.106 | 0.1041 | 0.1418 | RANDOM | 13.3 |
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] | |
-0.13 | -0.13 | 0.15 | -0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.958 |
r_sphericity_free | 31.522 |
r_dihedral_angle_4_deg | 20.737 |
r_dihedral_angle_3_deg | 12.06 |
r_sphericity_bonded | 12.039 |
r_dihedral_angle_1_deg | 6.352 |
r_rigid_bond_restr | 5.687 |
r_mcangle_it | 2.508 |
r_angle_refined_deg | 2.051 |
r_mcbond_it | 1.913 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2455 |
Nucleic Acid Atoms | |
Solvent Atoms | 490 |
Heterogen Atoms | 16 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XSCALE | data scaling |
PHASER | phasing |
XSCALE | data reduction |