8PNO
The MgF3(H2O) transition state analog complex of E. coli YihX
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2B0C |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 20 mg/mL YihX in Tris-HCl 25 mM pH 7.5, NaCl 150 mM, MgCl2 20 mM, NaF 30 mM was mixed 1:1 ratio with precipitant containing MES 55.5 mM, imidazole 44.5 mM pH 6.5, 20% PEG500, 30 mM MgCl2, 30 mM CaCl2, 20% glycerol, 10% PEG4000. The crystals are further soaked with the precipitant supplemented with 50 mM MgCl2 and 100 mM NH4F |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.43 | 71.97 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.259 | α = 90 |
b = 79.325 | β = 108.52 |
c = 80.297 | 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 | PIXEL | DECTRIS EIGER2 XE 16M | 2022-04-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9762 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.2 | 58.97 | 100 | 0.992 | 5.8 | 6.9 | 40811 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.2 | 2.27 | 0.664 | 1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.2 | 59.04 | 38765 | 2023 | 99.92 | 0.21376 | 0.21152 | 0.25711 | RANDOM | 38.806 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.33 | -0.56 | -3.87 | 3.74 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 15.471 |
r_dihedral_angle_2_deg | 8.552 |
r_long_range_B_refined | 7.69 |
r_long_range_B_other | 7.689 |
r_dihedral_angle_1_deg | 7.156 |
r_scangle_other | 5.431 |
r_mcangle_it | 4.802 |
r_mcangle_other | 4.801 |
r_scbond_it | 3.721 |
r_scbond_other | 3.721 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3196 |
Nucleic Acid Atoms | |
Solvent Atoms | 231 |
Heterogen Atoms | 111 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
Aimless | data scaling |
MOLREP | phasing |