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Alpha-conotoxin OmIA with unusual pharmacological properties at alpha7 nicotinic receptors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T90
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M ammonium sulfate, 5% PEG4000 and 0.1M sodium acetate trihydrate pH 4.6
Crystal Properties Matthews coefficient Solvent content 3.49 64.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.363 α = 90 b = 169.363 β = 90 c = 124.343 γ = 90
Symmetry Space Group P 4 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 100 PIXEL DECTRIS EIGER X 16M 2018-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 2.47 49.24 99.6 0.115 17.9 26.85 65087
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) 1 2.47 2.53 1.153
Refinement Statistics 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5T90 2.47 49.19 63054 2000 99.58 0.18748 0.18668 0.1956 0.21242 0.2176 RANDOM 31.052
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] 0.07 0.07 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.759 r_dihedral_angle_4_deg 18.672 r_dihedral_angle_3_deg 14.839 r_long_range_B_other 9.363 r_long_range_B_refined 9.358 r_dihedral_angle_1_deg 7.351 r_scangle_other 6.854 r_mcangle_other 5.155 r_mcangle_it 5.154 r_scbond_it 4.756
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.759 r_dihedral_angle_4_deg 18.672 r_dihedral_angle_3_deg 14.839 r_long_range_B_other 9.363 r_long_range_B_refined 9.358 r_dihedral_angle_1_deg 7.351 r_scangle_other 6.854 r_mcangle_other 5.155 r_mcangle_it 5.154 r_scbond_it 4.756 r_scbond_other 4.756 r_mcbond_it 3.564 r_mcbond_other 3.533 r_angle_refined_deg 1.685 r_angle_other_deg 1.102 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8717 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction Aimless data scaling PHENIX phasing