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Crystal structure of wild type Aplysia californica AChBP in complex with strychnine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XYS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Reservoir contained 0.1 M magnesium chloride, 25% PEG 3350. Protein buffer 50 mm tris, 250 mM NaCl, pH 7.5. 0.5 mM strychnine
Crystal Properties Matthews coefficient Solvent content 2.39 48.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.46 α = 90 b = 74.46 β = 90 c = 186.754 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 150 PIXEL DECTRIS PILATUS 6M-F 2015-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.91739 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 28.63 99.1 0.135 0.994 8.5 5.5 58318 23.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 99.7 0.762 0.552 2.3 5.7
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 2xys 2.2 28.63 55431 2828 99.05 0.18347 0.18116 0.189 0.22855 0.2333 RANDOM 35.142
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] -0.03 -0.01 -0.03 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.335 r_dihedral_angle_4_deg 17.688 r_dihedral_angle_3_deg 13.519 r_long_range_B_other 13.505 r_long_range_B_refined 13.472 r_scangle_other 12.267 r_scbond_it 9.536 r_scbond_other 9.532 r_mcangle_it 8.533 r_mcangle_other 8.533
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.335 r_dihedral_angle_4_deg 17.688 r_dihedral_angle_3_deg 13.519 r_long_range_B_other 13.505 r_long_range_B_refined 13.472 r_scangle_other 12.267 r_scbond_it 9.536 r_scbond_other 9.532 r_mcangle_it 8.533 r_mcangle_other 8.533 r_mcbond_it 6.651 r_mcbond_other 6.646 r_dihedral_angle_1_deg 6.409 r_angle_refined_deg 1.378 r_angle_other_deg 0.908 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_bond_other_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8202 Nucleic Acid Atoms Solvent Atoms 588 Heterogen Atoms 195
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing