8YQ8
Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS V1/S) complexed with FB8, NADPH and dUMP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4DP3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 4.6 | 297 | 0.1 M Sodium acetate, pH 4.6, 0.2 M Ammonium acetate, 12% Polyethylene glycol 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.59 | 52.55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.763 | α = 90 |
b = 156.41 | β = 90 |
c = 165.065 | 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 | CMOS | BRUKER PHOTON 100 | 2022-03-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER TURBO X-RAY SOURCE | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.1 | 26.1 | 99.32 | 0.082 | 0.998 | 13.5 | 5.9 | 88097 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.1 | 2.14 | 100 | 0.487 | 0.915 | 2.4 | 4.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.1 | 26.096 | 87705 | 4422 | 99.352 | 0.197 | 0.1945 | 0.2404 | RANDOM | 33.374 |
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] | |
-0.144 | 0.037 | 0.108 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 14.47 |
r_dihedral_angle_3_deg | 14.045 |
r_dihedral_angle_2_deg | 11.763 |
r_lrange_it | 8.301 |
r_lrange_other | 8.264 |
r_dihedral_angle_1_deg | 7.46 |
r_scangle_it | 5.847 |
r_scangle_other | 5.847 |
r_mcangle_it | 4.357 |
r_mcangle_other | 4.357 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8676 |
Nucleic Acid Atoms | |
Solvent Atoms | 588 |
Heterogen Atoms | 198 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PROTEUM PLUS | data collection |
Coot | model building |
PHASER | phasing |
PROTEUM PLUS | data reduction |
PROTEUM PLUS | data scaling |