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Crystal structure of Aplysia californica AChBP in complex with the neonicotinoid imidacloprid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BYN pdb entry 2byn
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 22% isopropanol, 0.2M magnesium chloride, 0.1 M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.54 51.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.39 α = 90 b = 116.286 β = 90 c = 132.463 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315 2006-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
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 2.48 47.72 97.7 0.095 18.8 2.1 46414 44102 42.7
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 2.48 2.57 98.1 0.45 4 5.8 7210
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 pdb entry 2byn 2.48 47.72 44045 2355 97.63 0.19084 0.18763 0.1919 0.25047 0.2512 RANDOM 39.48
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] -0.46 -1.09 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.336 r_dihedral_angle_4_deg 24.276 r_dihedral_angle_3_deg 17.631 r_dihedral_angle_1_deg 7.579 r_scangle_it 5.63 r_scbond_it 3.947 r_mcangle_it 2.395 r_angle_refined_deg 2.273 r_mcbond_it 1.53 r_symmetry_hbond_refined 0.577
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.336 r_dihedral_angle_4_deg 24.276 r_dihedral_angle_3_deg 17.631 r_dihedral_angle_1_deg 7.579 r_scangle_it 5.63 r_scbond_it 3.947 r_mcangle_it 2.395 r_angle_refined_deg 2.273 r_mcbond_it 1.53 r_symmetry_hbond_refined 0.577 r_nbtor_refined 0.329 r_nbd_refined 0.233 r_symmetry_vdw_refined 0.204 r_chiral_restr 0.152 r_xyhbond_nbd_refined 0.149 r_bond_refined_d 0.028 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8414 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling PHASER phasing