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Crystal structure of wild type Aplysia californica AChBP in complex with nicotine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XYS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.45 M ammonium phosphate monobasic
2 % glycerol
2 % IPA
Crystal Properties Matthews coefficient Solvent content 2.39 48.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 210.781 α = 90 b = 131.999 β = 103.15 c = 130.655 γ = 90
Symmetry Space Group C 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 150 CCD RIGAKU SATURN 944+ Varimax Cu-VHF 2016-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54157
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 2.2 25.2 99.9 0.115 0.993 8.8 6.8 176070 27.2
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 2.2 2.24 99.9 0.639 0.675 3.3 6.7
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 2xys 2.2 25.2 167118 8653 99.71 0.20444 0.20286 0.2132 0.23515 0.2437 RANDOM 34.896
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] -1.93 -0.24 1.53 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.957 r_dihedral_angle_4_deg 15.259 r_long_range_B_other 13.003 r_long_range_B_refined 12.976 r_scangle_other 12.036 r_dihedral_angle_3_deg 11.99 r_scbond_it 9.273 r_scbond_other 9.272 r_dihedral_angle_1_deg 8.205 r_mcangle_it 6.849
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.957 r_dihedral_angle_4_deg 15.259 r_long_range_B_other 13.003 r_long_range_B_refined 12.976 r_scangle_other 12.036 r_dihedral_angle_3_deg 11.99 r_scbond_it 9.273 r_scbond_other 9.272 r_dihedral_angle_1_deg 8.205 r_mcangle_it 6.849 r_mcangle_other 6.849 r_mcbond_it 5.902 r_mcbond_other 5.902 r_angle_refined_deg 1.451 r_angle_other_deg 0.972 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_bond_other_d 0.008 r_gen_planes_refined 0.006 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 16502 Nucleic Acid Atoms Solvent Atoms 1801 Heterogen Atoms 568
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing