6CXK
E. coli DHFR substrate complex with Dihydrofolate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7DFR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293.15 | Sitting drop of final volume of 0.8 uL was set up by 1:1 v/v mixing of 15 mg/mL E. coli DHFR working stock with reservoir solution containing 0.1M MES pH 6.5, 27.5% PEG 3350, 0.4M MgCl2. E. coli DHFR working stock was prepared from a 1:1 v/v mixture of 30 mg/ml protein in 20 mM Tris pH 8, 1mM DTT with 50 mM HEPES pH 7.3, 100 mM NaCl. Crystals harvested after 2 weeks growth and cryoprotected with mitegen LV oil before flash freezing in N2. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.78 | 31.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 33.698 | α = 90 |
b = 51.525 | β = 90 |
c = 77.421 | 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 | RAYONIX MX-225 | Diamond(111) | 2017-11-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.97931 | APS | 31-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.108 | 30.949 | 97.9 | 0.067 | 0.073 | 0.999 | 13.44 | 6.255 | 53265 | 11.47 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.108 | 1.18 | 87.3 | 0.861 | 1.051 | 0.571 | 1.16 | 2.804 |
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 | THROUGHOUT | 7DFR | 1.108 | 30.949 | 1.34 | 53202 | 1993 | 97.82 | 0.1792 | 0.1786 | 0.1961 | 18.63 |
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 | 13.574 |
f_angle_d | 1.334 |
f_chiral_restr | 0.078 |
f_bond_d | 0.009 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1328 |
Nucleic Acid Atoms | |
Solvent Atoms | 202 |
Heterogen Atoms | 60 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |