2PRL
The structures of apo- and inhibitor bound human dihydroorotate dehydrogenase reveal conformational flexibility within the inhibitor binding site
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1D3G |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.8 | 293 | DROPS WERE FORMED BY MIXING EQUAL AMOUNTS OF 18-24 MG/ML PROTEIN IN 100 MM HEPES PH 7.0, 400 MM NACL, 30% GLYCEROL, 1 MM EDTA AND 10 MM N,N- DIMETHYLUNDECYLAMIN-N-OXIDE (C11DAO) WITH A PRECIPITANT SOLUTION OF 0.1 M ACETATE PH 4.8 40 MM C11DAO, 20.8 MM N,-DIMETHYLDECYLAMINE-N-OXIDE (DDAO), 2 MM DIHYDROOROTATE (DHO) THE HANGING DROPS WERE INCUBATED AGAINST 0.5 ML RESERVOIR OF 0.1 M ACETATE PH 4.8, 1.6-2.2 M AMMONIUM SULFATE AND 30% GLYCEROL., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.61 | 65.94 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 90.41 | α = 90 |
b = 90.41 | β = 90 |
c = 122.07 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 1 |
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 | IMAGE PLATE | MAR scanner 345 mm plate | mirrors | 2004-04-27 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I711 | 1.092 | MAX II | I711 |
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 | ||||||||
1,2 | 2.1 | 18.83 | 98 | 0.114 | 12.17 | 33570 | -3 | 22.487 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1,2 | 2.1 | 2.2 | 99.5 | 0.327 | 5.8 | 4367 |
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 | 1d3g | 2.1 | 18.83 | 31888 | 1678 | 0.16907 | 0.16771 | 0.19441 | RANDOM | 10.597 |
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] | |
0.16 | 0.08 | 0.16 | -0.25 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.984 |
r_dihedral_angle_4_deg | 18.191 |
r_dihedral_angle_3_deg | 12.664 |
r_dihedral_angle_1_deg | 5.696 |
r_scangle_it | 2.081 |
r_angle_refined_deg | 1.298 |
r_scbond_it | 1.27 |
r_mcangle_it | 0.755 |
r_mcbond_it | 0.487 |
r_nbtor_refined | 0.306 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2805 |
Nucleic Acid Atoms | |
Solvent Atoms | 231 |
Heterogen Atoms | 94 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
REFMAC | refinement |
REFMAC | refinement |
MAR345dtb | data collection |
XDS | data reduction |
XSCALE | data scaling |
CNS | phasing |