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Crystal structure of Aplysia californica AChBP in complex with epibatidine
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 7.5 18-22% PEG-3350, 0.1 M TRIS, PH 7.5, 0.2 M SODIUM CITRATE
Crystal Properties Matthews coefficient Solvent content 2.81 55.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 200.925 α = 90 b = 200.925 β = 90 c = 200.925 γ = 90
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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 3.4 30 97.6 0.19 8.3 3.5 18257
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 3.4 30 17132 929 96.8 0.184 0.18 0.1854 0.255 0.2496 RANDOM 45.41
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.159 r_dihedral_angle_3_deg 20.471 r_dihedral_angle_4_deg 18.45 r_dihedral_angle_1_deg 7.472 r_angle_refined_deg 1.524 r_scangle_it 1.292 r_scbond_it 0.772 r_mcangle_it 0.482 r_nbtor_refined 0.319 r_mcbond_it 0.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.159 r_dihedral_angle_3_deg 20.471 r_dihedral_angle_4_deg 18.45 r_dihedral_angle_1_deg 7.472 r_angle_refined_deg 1.524 r_scangle_it 1.292 r_scbond_it 0.772 r_mcangle_it 0.482 r_nbtor_refined 0.319 r_mcbond_it 0.271 r_symmetry_vdw_refined 0.256 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.104 r_symmetry_hbond_refined 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 8515 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALA data scaling AMoRE phasing