4WBR
Structure of Bradyrhizobium japonicum ScoI with copper bound
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 | 5 | 293 | 0.1 M Na-citrate, 20% PEG 6000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 92.86 | α = 90 |
b = 44.76 | β = 90 |
c = 40 | γ = 90 |
Symmetry | |
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Space Group | P 21 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 | 80 | PIXEL | DECTRIS PILATUS 6M | 2014-07-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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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 | 1.4 | 46 | 91.2 | 0.099 | 0.103 | 17.04 | 12 | 30788 | -3 | 19.097 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.4 | 1.43 | 55.9 | 0.763 | 0.809 | 2.33 |
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 | 1.4 | 42 | 30788 | 1494 | 91.2 | 0.1283 | 0.126 | 0.1753 | RANDOM | 18.926 |
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] | |
0.47 | -0.27 | -0.2 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 49.923 |
r_dihedral_angle_2_deg | 33.436 |
r_dihedral_angle_4_deg | 18.667 |
r_sphericity_bonded | 14.632 |
r_dihedral_angle_3_deg | 13.459 |
r_dihedral_angle_1_deg | 5.793 |
r_rigid_bond_restr | 5.405 |
r_mcangle_it | 3.779 |
r_mcbond_it | 3.729 |
r_mcbond_other | 3.721 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1225 |
Nucleic Acid Atoms | |
Solvent Atoms | 235 |
Heterogen Atoms | 1 |
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 |