4FJ0
Crystal structure of the ternary complex between a fungal 17beta-hydroxysteroid dehydrogenase (Holo form) and 3,7-dihydroxy flavone
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3QWI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 30% (W/V) PEG 2000 MME, 0.1M KCNS, 5 mM NADP. Crystals soaked for 24 hours in: 30% (W/V) PEG 2000 MME, 0.1M KCNS, 15% (V/V)ETHYLENE GLYCOLE, 5% (V/V) DMSO, 1 mM NADP, 0.8 mM 3,7-dihydroxyflavone, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.06 | 40.34 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.34 | α = 90 |
b = 113.25 | β = 102.76 |
c = 69.31 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | PIXEL | DECTRIS PILATUS 2M | Platinum coated cylindrical mirror | 2010-07-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 5.2R | 1.2 | ELETTRA | 5.2R |
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 | 45 | 95.1 | 0.079 | 11.8 | 3.5 | 45372 | 45372 | -3 | 35 |
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 | 2.33 | 82.4 | 0.267 | 3.71 | 2.65 | 6010 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3QWI | 2.2 | 43.41 | 43102 | 43102 | 2269 | 95.2 | 0.17173 | 0.17173 | 0.16997 | 0.20469 | RANDOM | 24.731 |
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] | |
-0.67 | -1.71 | 1.25 | -1.34 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.952 |
r_dihedral_angle_3_deg | 13.676 |
r_dihedral_angle_4_deg | 8.852 |
r_dihedral_angle_1_deg | 5.689 |
r_angle_refined_deg | 1.389 |
r_angle_other_deg | 1.208 |
r_chiral_restr | 0.081 |
r_bond_refined_d | 0.01 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7851 |
Nucleic Acid Atoms | |
Solvent Atoms | 270 |
Heterogen Atoms | 262 |
Software
Software | |
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Software Name | Purpose |
XRD1 | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |