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Crystal structure of a complex of AChBP from aplysia californica and the neonicotinoid thiacloprid
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 30% isopropanol, 0.2M magnesium chloride, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.53 51.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.893 α = 90 b = 116.726 β = 90 c = 132.002 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 1.94 87.4 99.9 0.078 21 6.4 97540 94127
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 1.94 2.01 100 0.491 4.1 6.1 9613
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1.94 87.37 97540 92566 4876 99.73 0.18747 0.18602 0.1906 0.21501 0.2169 RANDOM 32.539
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] -0.75 -1.09 1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.974 r_dihedral_angle_4_deg 18.932 r_dihedral_angle_3_deg 12.429 r_dihedral_angle_1_deg 6.442 r_scangle_it 3.977 r_scbond_it 2.774 r_mcangle_it 1.694 r_angle_refined_deg 1.495 r_mcbond_it 1.152 r_symmetry_hbond_refined 0.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.974 r_dihedral_angle_4_deg 18.932 r_dihedral_angle_3_deg 12.429 r_dihedral_angle_1_deg 6.442 r_scangle_it 3.977 r_scbond_it 2.774 r_mcangle_it 1.694 r_angle_refined_deg 1.495 r_mcbond_it 1.152 r_symmetry_hbond_refined 0.327 r_nbtor_refined 0.307 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.159 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.108 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8309 Nucleic Acid Atoms Solvent Atoms 478 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling PHASER phasing