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Structure of Pectenotoxin-2 Bound to Actin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ASO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 100 mM Na/MES/acetate, pH 5.5, 15% methyl ether poly(ethylene glycol) 5000, 10% hexanediol, 30 mM CaCl2, and 1 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.437 α = 90 b = 56.856 β = 90.16 c = 105.747 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 CCD SBC Rosenbaum-Rock double-crystal monochromator: Water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror 2006-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.96411 APS 19-BM
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 1.7 45 97.2 0.04 14.4 4.2 37755 23.4
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) 1.7 1.76 93.4 0.109 9.5 3.9 3595
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 2ASO 1.7 45 157276 37752 1887 96.98 0.17 0.168 0.1791 0.204 0.2108 RANDOM 14.099
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] 0.65 -0.02 -0.92 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.838 r_dihedral_angle_4_deg 17.102 r_dihedral_angle_3_deg 12.715 r_dihedral_angle_1_deg 5.498 r_scangle_it 3.011 r_scbond_it 2.069 r_angle_refined_deg 1.772 r_angle_other_deg 1.321 r_mcangle_it 1.269 r_mcbond_it 0.822
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.838 r_dihedral_angle_4_deg 17.102 r_dihedral_angle_3_deg 12.715 r_dihedral_angle_1_deg 5.498 r_scangle_it 3.011 r_scbond_it 2.069 r_angle_refined_deg 1.772 r_angle_other_deg 1.321 r_mcangle_it 1.269 r_mcbond_it 0.822 r_symmetry_vdw_refined 0.393 r_nbd_refined 0.22 r_symmetry_vdw_other 0.22 r_mcbond_other 0.2 r_nbd_other 0.187 r_nbtor_refined 0.181 r_symmetry_hbond_refined 0.167 r_xyhbond_nbd_refined 0.159 r_nbtor_other 0.089 r_chiral_restr 0.087 r_metal_ion_refined 0.079 r_symmetry_metal_ion_refined 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2780 Nucleic Acid Atoms Solvent Atoms 386 Heterogen Atoms 96
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data collection HKL-3000 data reduction