8BAX
X-ray structure of the CeuE Homologue from Geobacillus stearothermophilus - azotochelin complex.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8BPX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | Morph C8: 12.5% PEG1K; 12.5% PEG 3350; 12.5% MPD; 0.03M each NPS (NaNO3, Na2HPO4, (NH4)2SO4); 0.1M MOPS/HEPES pH7.5. Ligand: 1.67mM Fe azotochelin-sulf/pyr-Ir catalyst, 1:1 protein:ligand ratio. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 38.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 34.158 | α = 90 |
b = 66.652 | β = 90 |
c = 117.055 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | PIXEL | DECTRIS EIGER2 S 16M | 2022-07-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97628 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 58.596 | 97.5 | 0.128 | 0.138 | 0.051 | 0.998 | 8.2 | 13.6 | 54541 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.38 | 1.4 | 4.439 | 4.775 | 1.752 | 0.473 | 14.2 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 8BPX | 1.38 | 58.596 | 54461 | 2753 | 97.353 | 0.217 | 0.2141 | 0.2622 | 30.655 |
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] | |
-3.51 | -4.427 | 7.937 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_rigid_bond_restr | 22.582 |
r_dihedral_angle_6_deg | 15.601 |
r_dihedral_angle_3_deg | 14.992 |
r_lrange_other | 7.391 |
r_lrange_it | 7.386 |
r_scangle_it | 7.301 |
r_scangle_other | 7.299 |
r_mcangle_other | 6.837 |
r_mcangle_it | 6.834 |
r_scbond_other | 6.831 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2214 |
Nucleic Acid Atoms | |
Solvent Atoms | 95 |
Heterogen Atoms | 31 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
REFMAC | refinement |
DIALS | data reduction |
Aimless | data scaling |
MOLREP | phasing |