5VPN
E. coli Quinol fumarate reductase FrdA E245Q mutation
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1L0V |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | Crystals of the QFR-FrdAE245Q mutant were grown using the hanging-drop vapor diffusion method in droplets containing protein solution (15 mg/ml QFR FrdAE245Q in 25 mM Tris-HCl pH 7.4, 1 mM EDTA, 0.02 % C12E9) and the reservoir solution (275 mM NaMalonate, 19% polyethylene glycol 6000, 100 mM NaCitrate pH 4.0, 1 mM EDTA and 0.001% dithiothreitol) in a 1:1 ratio. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.25 | 71.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 133.565 | α = 90 |
b = 138.134 | β = 90 |
c = 220.079 | 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 | CCD | MARMOSAIC 225 mm CCD | 2014-10-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.9798 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 4.22 | 50 | 96.8 | 1.4 | 5.5 | 28494 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation 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 | FREE R-VALUE | 1L0V | 4.2232 | 22.962 | 1.33 | 28494 | 1417 | 95.93 | 0.2176 | 0.2148 | 0.2704 | 214.5661 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.842 |
f_angle_d | 0.614 |
f_chiral_restr | 0.042 |
f_plane_restr | 0.005 |
f_bond_d | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 16701 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 144 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data scaling |
PHASER | phasing |