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Crystal structure of Lymnaea stagnalis Acetylcholine-binding protein (Ls-AChBP) Q55R/M114V double mutant complexed with Sulfoxaflor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UV6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 14-18% PEG3350, 0.1-0.25M diammonium hydrogen citrate, 15% glycerol
Crystal Properties Matthews coefficient Solvent content 2.3 46.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.886 α = 90 b = 74.367 β = 101.645 c = 130.058 γ = 90
Symmetry Space Group P 1 2 1
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 PILATUS3 6M 2020-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96864 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.796 127.381 95 0.11 0.997 9.9 6.7 117528
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.796 2.034 1.097 0.613
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1UV6 2 127.381 113516 5524 77.418 0.208 0.2063 0.2117 0.2311 0.2329 38.199
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] -1.233 0.254 0.054 0.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.961 r_dihedral_angle_4_deg 17.476 r_dihedral_angle_3_deg 14.726 r_dihedral_angle_1_deg 7.756 r_lrange_it 5.532 r_lrange_other 5.529 r_scangle_it 3.341 r_scangle_other 3.341 r_mcangle_it 2.284 r_mcangle_other 2.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.961 r_dihedral_angle_4_deg 17.476 r_dihedral_angle_3_deg 14.726 r_dihedral_angle_1_deg 7.756 r_lrange_it 5.532 r_lrange_other 5.529 r_scangle_it 3.341 r_scangle_other 3.341 r_mcangle_it 2.284 r_mcangle_other 2.283 r_scbond_it 2.019 r_scbond_other 2.019 r_angle_refined_deg 1.869 r_mcbond_it 1.385 r_mcbond_other 1.385 r_angle_other_deg 1.364 r_nbd_other 0.239 r_nbd_refined 0.194 r_symmetry_nbd_refined 0.192 r_symmetry_xyhbond_nbd_refined 0.188 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.162 r_ncsr_local_group_20 0.111 r_ncsr_local_group_13 0.106 r_ncsr_local_group_36 0.106 r_ncsr_local_group_37 0.105 r_ncsr_local_group_11 0.102 r_ncsr_local_group_26 0.102 r_ncsr_local_group_2 0.101 r_ncsr_local_group_38 0.101 r_ncsr_local_group_12 0.1 r_ncsr_local_group_6 0.099 r_ncsr_local_group_17 0.099 r_symmetry_xyhbond_nbd_other 0.098 r_ncsr_local_group_31 0.098 r_ncsr_local_group_16 0.097 r_ncsr_local_group_1 0.096 r_ncsr_local_group_39 0.096 r_ncsr_local_group_7 0.094 r_ncsr_local_group_41 0.094 r_ncsr_local_group_10 0.093 r_ncsr_local_group_15 0.093 r_ncsr_local_group_18 0.093 r_ncsr_local_group_19 0.092 r_ncsr_local_group_23 0.092 r_ncsr_local_group_43 0.092 r_ncsr_local_group_27 0.091 r_ncsr_local_group_3 0.089 r_ncsr_local_group_21 0.088 r_ncsr_local_group_34 0.087 r_ncsr_local_group_42 0.087 r_ncsr_local_group_8 0.086 r_ncsr_local_group_9 0.085 r_ncsr_local_group_24 0.085 r_ncsr_local_group_45 0.085 r_ncsr_local_group_28 0.084 r_ncsr_local_group_4 0.083 r_ncsr_local_group_32 0.083 r_ncsr_local_group_40 0.082 r_chiral_restr 0.081 r_ncsr_local_group_25 0.081 r_ncsr_local_group_33 0.08 r_ncsr_local_group_44 0.08 r_symmetry_nbtor_other 0.079 r_ncsr_local_group_30 0.079 r_ncsr_local_group_5 0.071 r_ncsr_local_group_14 0.069 r_ncsr_local_group_22 0.066 r_ncsr_local_group_35 0.065 r_ncsr_local_group_29 0.05 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15947 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 162
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling MOLREP phasing