8G7H
Crystal Structure of FosB from Bacillus cereus with Zinc and (1-hydroxypropan-2-yl)phosphonic acid
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4JH6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 298 | Protein solution (10 mg/mL FosB in 20 mM HEPES buffer, pH 7.5 and 5 mM inhibitor) and reservoir solution (75 mM Mg formate and 14% (w/v) PEG 3350) were mixed in a Hampton Research VDX plate using a 2:3 ratio of protein:reservoir solutions. Cryoprotected in its reservoir solution with 20% glycerol added prior to rapid freezing in liquid nitrogen |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.24 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 64.233 | ¦Á = 90 |
b = 68.21 | ¦Â = 90 |
c = 69.826 | ¦Ã = 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 EIGER X 16M | 2022-09-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0 | APS | 22-ID |
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 | 1.81 | 50 | 99.9 | 0.138 | 0.145 | 0.044 | 0.994 | 4.1 | 10.7 | 28683 |
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) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.81 | 1.84 | 100 | 0.785 | 0.829 | 0.263 | 0.841 | 9.5 |
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 (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4JH6 | 1.81 | 48.793 | 28626 | 1462 | 99.725 | 0.156 | 0.1543 | 0.1852 | RANDOM | 19.454 |
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] | |
0.002 | -0.004 | 0.002 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 17.519 |
r_dihedral_angle_3_deg | 13.282 |
r_dihedral_angle_1_deg | 6.897 |
r_lrange_it | 6.454 |
r_lrange_other | 6.342 |
r_dihedral_angle_2_deg | 5.582 |
r_scangle_it | 4.495 |
r_scangle_other | 4.493 |
r_scbond_it | 2.835 |
r_scbond_other | 2.834 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2324 |
Nucleic Acid Atoms | |
Solvent Atoms | 270 |
Heterogen Atoms | 47 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALEPACK | data scaling |
PHASER | phasing |
HKL-2000 | data reduction |