☰ Navigation Tabs
Aplysia californica AChBP in complex with a cytisine derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QKK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295.15 Starting protein concentration 12.5 mg/ml + 6 mM ligand BS82.
Crystallised as hanging drops, the drop containing 1.5 ul protein, 0.2 ul reservoir (0.8 M NaH2PO4, 0.8 M KH2PO4, 10% glycerol, 0.1 M HEPES pH 7.0) and 0.3 ul microseeds from cytisine bound AChBP crystals (grown as sitting drops in 0.8 M NaH2PO4, 0.8 M KH2PO4, 0.1 M HEPES pH 7.5).
Crystal Properties Matthews coefficient Solvent content 3.14 60.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 209.466 α = 90 b = 132.874 β = 102.524 c = 131.086 γ = 90
Symmetry Space Group C 1 2 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 EIGER2 X 16M 2019-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.72 127.97 95.5 0.07 0.095 0.064 0.993 7.6 3.5 353432 25.07
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.75 66.6 0.82 1.138 0.787 0.435 0.6 2.1
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-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6QKK 1.72 111.666 353365 17388 95.459 0.163 0.1619 0.1922 0.1926 30.393
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] -2.078 -0.075 2.651 -0.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.528 r_dihedral_angle_4_deg 20.452 r_dihedral_angle_1_deg 19.702 r_dihedral_angle_3_deg 13.707 r_lrange_it 8.358 r_lrange_other 8.106 r_scangle_it 6.038 r_scangle_other 6.038 r_scbond_it 4.143 r_scbond_other 4.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.528 r_dihedral_angle_4_deg 20.452 r_dihedral_angle_1_deg 19.702 r_dihedral_angle_3_deg 13.707 r_lrange_it 8.358 r_lrange_other 8.106 r_scangle_it 6.038 r_scangle_other 6.038 r_scbond_it 4.143 r_scbond_other 4.143 r_mcangle_it 3.62 r_mcangle_other 3.62 r_mcbond_it 2.665 r_mcbond_other 2.665 r_angle_other_deg 2.474 r_angle_refined_deg 1.838 r_symmetry_nbd_refined 0.227 r_symmetry_nbd_other 0.199 r_nbd_other 0.189 r_nbd_refined 0.188 r_xyhbond_nbd_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.164 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.086 r_metal_ion_refined 0.084 r_symmetry_xyhbond_nbd_other 0.067 r_bond_other_d 0.034 r_gen_planes_other 0.016 r_bond_refined_d 0.013 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16425 Nucleic Acid Atoms Solvent Atoms 2899 Heterogen Atoms 636
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing