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Assembly of a triple pi-stack of ligands in the binding site of Aplysia californica acetylcholine binding protein (AChBP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W8E PDB ENTRY 2W8E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 292 THE VUF9432-AC-ACHBP COMPLEX WAS FORMED BY MIXING THE PROTEIN AT 3.5 MG/ML WITH 1MM VUF9432 AND INCUBATING ON ICE FOR 1 HOUR. CRYSTALS WERE GROWN USING THE VAPOUR DIFFUSION METHOD IN A SOLUTION CONSISTING OF 0.2M LISO4, 0.8M AMMONIUM SULPHATE IN MMT BUFFER (PH 8.0) AND 19 DEGREES C
Crystal Properties Matthews coefficient Solvent content 2.86 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.73 α = 90 b = 78.33 β = 102.67 c = 106.53 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2010-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.4 43.3 93 0.13 5.9 2.4 47324
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 2.4 2.53 92.6 0.76 1.8 2.4
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 2W8E 2.4 41.26 44879 2422 92.86 0.21156 0.20964 0.2109 0.24724 0.2439 RANDOM 37.833
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] 0.68 -0.93 -0.61 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.917 r_dihedral_angle_4_deg 16.053 r_dihedral_angle_3_deg 12.484 r_dihedral_angle_1_deg 6.292 r_angle_refined_deg 1.315 r_angle_other_deg 1.216 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.917 r_dihedral_angle_4_deg 16.053 r_dihedral_angle_3_deg 12.484 r_dihedral_angle_1_deg 6.292 r_angle_refined_deg 1.315 r_angle_other_deg 1.216 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.005 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_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 8180 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 384
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing