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Structure of Pectenotoxin-2 and Latrunculin B 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, 100 mM CaCl2, and 1 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.98 37.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.683 α = 90 b = 54.342 β = 90.27 c = 105.895 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 1.41 50 96.6 0.04 10.1 4.6 60883 19
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) 1.41 1.46 84.9 0.136 5.7 4.1 5315
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 2ASO 1.45 45 56889 2891 97.81 0.166 0.165 0.1665 0.181 0.1834 RANDOM 11.813
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] 0.35 0.06 -0.14 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.015 r_dihedral_angle_4_deg 18.164 r_dihedral_angle_3_deg 11.183 r_dihedral_angle_1_deg 5.411 r_scangle_it 2.14 r_angle_refined_deg 1.678 r_scbond_it 1.59 r_angle_other_deg 1.164 r_mcangle_it 1.075 r_mcbond_it 0.664
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.015 r_dihedral_angle_4_deg 18.164 r_dihedral_angle_3_deg 11.183 r_dihedral_angle_1_deg 5.411 r_scangle_it 2.14 r_angle_refined_deg 1.678 r_scbond_it 1.59 r_angle_other_deg 1.164 r_mcangle_it 1.075 r_mcbond_it 0.664 r_symmetry_hbond_refined 0.239 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.208 r_nbd_other 0.191 r_symmetry_vdw_other 0.184 r_nbtor_refined 0.179 r_chiral_restr 0.173 r_xyhbond_nbd_refined 0.153 r_mcbond_other 0.135 r_symmetry_metal_ion_refined 0.096 r_nbtor_other 0.085 r_metal_ion_refined 0.082 r_gen_planes_refined 0.01 r_bond_refined_d 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2717 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 121
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