5KTC
FdhC with bound products: Coenzyme A and 3-[(R)-3-hydroxybutanoylamino]-3,6-dideoxy-d-galactose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5KTA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 5 | 277 | 30% monomethylether poly(ethylene glycol) 5000, 200 mM LiCl, and 100 mM Homo-PIPES |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.53 | 51.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.268 | α = 90 |
b = 76.268 | β = 90 |
c = 73.47 | γ = 90 |
Symmetry | |
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Space Group | P 41 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 | 100 | CCD | Bruker Platinum 135 | 2016-05-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 |
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 | 1.8 | 50 | 98.2 | 0.074 | 17.6 | 9.5 | 20344 |
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 | 5kta | 1.8 | 50 | 19260 | 1043 | 98.25 | 0.19664 | 0.19393 | 0.24746 | RANDOM | 20.766 |
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] | |
0.82 | 0.82 | -1.63 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.961 |
r_dihedral_angle_4_deg | 17.593 |
r_dihedral_angle_3_deg | 15.209 |
r_dihedral_angle_1_deg | 7.509 |
r_long_range_B_refined | 5.598 |
r_long_range_B_other | 5.596 |
r_scangle_other | 4.137 |
r_mcangle_other | 2.858 |
r_mcangle_it | 2.857 |
r_scbond_it | 2.688 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1570 |
Nucleic Acid Atoms | |
Solvent Atoms | 148 |
Heterogen Atoms | 94 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SAINT | data reduction |
SADABS | data scaling |
PHASER | phasing |