6NY0
Crystal structure of trimethoprim-resistant type II dihydrofolate reductase in complex with a bisbenzimidazole inhibitor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2RH2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 277 | The protein was concentrated to 20 mg/mL in 100 mM Tris pH 8.0. Immediately before crystallization, chymotrypsin was added to the sample in a ratio of 1:100 chymotrypsin:protein, and the protein was diluted to 15 mg/mL using MPD, resulting in a final MPD concentration of 25%. Reservoirs were prepared using 750 uL of 100 mM sodium phosphate pH 7.6 and 60% MPD in a Greiner 24-well hanging-drop crystallization plate. On a siliconized glass cover slip (Hampton Research), 1.5 uL of protein were combined with 2.5 uL of reservoir solution and suspended over the well. The plate was incubated at 277 K and crystals were obtained in a few days. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.66 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.492 | α = 90 |
b = 67.492 | β = 90 |
c = 51.791 | γ = 90 |
Symmetry | |
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Space Group | I 41 2 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 | 93 | CCD | RAYONIX MX300HE | Vertical Focusing Mirror: ultra-low expansion (ULE) titanium siliicate flat mirror with Pt, Uncoated, and Pd strips | 2011-08-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | 0.9795 | CLSI | 08ID-1 |
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 | 1.35 | 50 | 100 | 0.102 | 8.8 | 20.1 | 13545 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.35 | 1.37 | 100 | 14.6 |
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 | 2RH2 | 1.4 | 41.09 | 11543 | 624 | 99.62 | 0.142 | 0.1412 | 0.1577 | RANDOM | 15.229 |
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 |
r_dihedral_angle_2_deg | 28.445 |
r_dihedral_angle_4_deg | 14.013 |
r_dihedral_angle_3_deg | 13.03 |
r_dihedral_angle_1_deg | 6.205 |
r_angle_other_deg | 2.328 |
r_angle_refined_deg | 2.076 |
r_chiral_restr | 0.117 |
r_bond_refined_d | 0.018 |
r_gen_planes_refined | 0.018 |
r_bond_other_d | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 437 |
Nucleic Acid Atoms | |
Solvent Atoms | 72 |
Heterogen Atoms | 31 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
REFMAC | phasing |