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Crystal Structure of Lymnaea stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Dinotefuran
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZJU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.4 293 PEG4000 16.5 - 18.0% , sodium citrate 0.2M
Crystal Properties Matthews coefficient Solvent content 2.36 47.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.149 α = 90 b = 74.149 β = 90 c = 350.306 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX225HE 2017-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.63 47.34 99.9 0.094 0.103 0.043 0.999 22 11.3 32196
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.63 2.76 99.7 0.827 0.91 0.379 0.949 11.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.632 47.34 32089 1629 99.888 0.198 0.1955 0.1976 0.2538 0.254 73.292
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] 1.997 0.998 1.997 -6.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.771 r_dihedral_angle_6_deg 13.395 r_lrange_it 8.904 r_lrange_other 8.904 r_dihedral_angle_2_deg 8.556 r_dihedral_angle_1_deg 7.455 r_scangle_it 5.647 r_scangle_other 5.646 r_mcangle_it 5.235 r_mcangle_other 5.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.771 r_dihedral_angle_6_deg 13.395 r_lrange_it 8.904 r_lrange_other 8.904 r_dihedral_angle_2_deg 8.556 r_dihedral_angle_1_deg 7.455 r_scangle_it 5.647 r_scangle_other 5.646 r_mcangle_it 5.235 r_mcangle_other 5.235 r_scbond_it 3.519 r_scbond_other 3.518 r_mcbond_it 3.232 r_mcbond_other 3.232 r_angle_refined_deg 1.527 r_angle_other_deg 0.542 r_nbd_other 0.26 r_symmetry_nbd_refined 0.221 r_nbd_refined 0.216 r_symmetry_nbd_other 0.199 r_symmetry_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.169 r_ncsr_local_group_10 0.124 r_ncsr_local_group_6 0.123 r_ncsr_local_group_8 0.119 r_ncsr_local_group_3 0.115 r_ncsr_local_group_9 0.114 r_ncsr_local_group_2 0.11 r_ncsr_local_group_5 0.109 r_ncsr_local_group_7 0.102 r_symmetry_nbtor_other 0.099 r_ncsr_local_group_4 0.095 r_ncsr_local_group_1 0.094 r_symmetry_xyhbond_nbd_other 0.088 r_chiral_restr 0.075 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8285 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 140
Software Software Software Name Purpose XDS data scaling XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement