2X0E
Complex structure of WsaF with dTDP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2X0D | PDB ENTRY 2X0D |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 293 | 0.2 MM MG FORMATE, 20% PEG3350, 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 75.82 | α = 90 |
b = 75.56 | β = 103.05 |
c = 77.71 | 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 | CCD | RIGAKU-MSC SATURN 944 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.81 | 29.6 | 95.1 | 0.08 | 13.6 | 1.9 | 38750 | 2.55 | 32.89 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.81 | 2.91 | 68.3 | 0.44 | 2.55 | 1.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 2X0D | 2.81 | 29.63 | 0.96 | 38728 | 1971 | 95.2 | 0.188 | 0.185 | 0.245 | 34.9 |
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] | |
-8.0703 | -3.0078 | 9.0152 | -0.9449 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.764 |
f_angle_d | 0.809 |
f_chiral_restr | 0.057 |
f_bond_d | 0.004 |
f_plane_restr | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6193 |
Nucleic Acid Atoms | |
Solvent Atoms | 114 |
Heterogen Atoms | 68 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |