☰ Navigation Tabs
hemipteran ecdysone receptor ligand-binding domain complexed with ponasterone A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DKF Homology model derived from pdb entry 1DKF
Crystallization Crystalization Experiments 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 Matthews coefficient Solvent content 4.35 71.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.005 α = 90 b = 143.005 β = 90 c = 84.015 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment 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 ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall 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 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 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) 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 0.2007 0.276 0.2694 RANDOM 46.2
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] -9.41 -9.41 18.82
RMS Deviations 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
RMS Deviations 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 c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3473 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 53
Software Software Software Name Purpose CNS refinement SCALEPACK data scaling CCP4 phasing