1Z5X
hemipteran ecdysone receptor ligand-binding domain complexed with ponasterone A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1DKF | Homology model derived from pdb entry 1DKF |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 1 M ammonium phosphate, 4.5 % trehalose, 10 mM DTT, 10 % glycerol, 3 mM ponasterone A, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.35 | 71.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 143.005 | α = 90 |
b = 143.005 | β = 90 |
c = 84.015 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 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 | 115 | IMAGE PLATE | RIGAKU RAXIS IV | Yale-MSC mirrors | 2002-02-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 3.07 | 27.48 | 99.7 | 0.13 | 19.3 | 11.4 | 16756 | 16756 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
3.07 | 3.11 | 99 | 0.51 | 5.6 | 10.5 | 2713 |
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 | Homology model derived from pdb entry 1DKF | 3.07 | 27.48 | 16740 | 16740 | 843 | 99.7 | 0.205 | 0.205 | 0.205 | 0.276 | RANDOM | 46.2 |
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] | |
-9.41 | -9.41 | 18.82 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 19.7 |
c_angle_deg | 1.6 |
c_improper_angle_d | 1.07 |
c_bond_d | 0.012 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d | |
c_angle_d_na | |
c_angle_d_prot | |
c_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3473 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 53 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
SCALEPACK | data scaling |
CCP4 | phasing |