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Crystal structure of Lymnaea stagnalis Acetylcholine binding protein (AChBP) complexed with Paraherquamide A
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 5 298 14.1-15.6% PEG 4000, Sodium Citrate buffer pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.4 48.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.373 α = 90 b = 74.373 β = 90 c = 349.595 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 2017-04-15 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) 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 47.374 100 0.071 21.7 10.8 55263
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 100 0.713 7.1
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2ZJU 2.2 47.37 55135 2734 99.9 0.185 0.1845 0.231 0.2307 49.02
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] 0.565 0.282 0.565 -1.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.391 r_dihedral_angle_4_deg 16.604 r_dihedral_angle_3_deg 14.299 r_dihedral_angle_1_deg 7.481 r_mcangle_it 1.571 r_mcangle_other 1.571 r_angle_refined_deg 1.413 r_scangle_it 1.254 r_scangle_other 1.254 r_angle_other_deg 1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.391 r_dihedral_angle_4_deg 16.604 r_dihedral_angle_3_deg 14.299 r_dihedral_angle_1_deg 7.481 r_mcangle_it 1.571 r_mcangle_other 1.571 r_angle_refined_deg 1.413 r_scangle_it 1.254 r_scangle_other 1.254 r_angle_other_deg 1.15 r_mcbond_it 0.872 r_mcbond_other 0.872 r_scbond_it 0.707 r_scbond_other 0.707 r_nbd_refined 0.169 r_nbd_other 0.159 r_nbtor_refined 0.158 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.048 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbtor_other 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_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8176 Nucleic Acid Atoms Solvent Atoms 486 Heterogen Atoms 250
Software Software Software Name Purpose REFMAC refinement XDS data processing XDS data reduction Aimless data scaling PHASER phasing Coot model building