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Crystal structure of tarantula venom peptide Protoxin-II
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 2M lithium sulfate, 100 mM Tris-HCl (pH 8), 2% v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 1.85 33.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.669 α = 90 b = 37.669 β = 90 c = 103.944 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 93 PIXEL DECTRIS PILATUS3 S 6M 2016-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0000 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 0.99 34.67 92.9 0.062 0.02 0.998 25 8.7 14967
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.993 1.01 43.3 0.496 0.361 0.7 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SIRAS THROUGHOUT 0.99 34.65 14235 732 92.88 0.12668 0.12601 0.13985 0.1541 RANDOM 13.675
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] -0.02 -0.01 -0.02 0.06
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 44.705 r_dihedral_angle_2_deg 34.913 r_sphericity_bonded 12.61 r_dihedral_angle_4_deg 11.561 r_dihedral_angle_3_deg 11 r_dihedral_angle_1_deg 6.192 r_long_range_B_refined 3.75 r_long_range_B_other 3.734 r_angle_other_deg 3.505 r_rigid_bond_restr 2.904
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 44.705 r_dihedral_angle_2_deg 34.913 r_sphericity_bonded 12.61 r_dihedral_angle_4_deg 11.561 r_dihedral_angle_3_deg 11 r_dihedral_angle_1_deg 6.192 r_long_range_B_refined 3.75 r_long_range_B_other 3.734 r_angle_other_deg 3.505 r_rigid_bond_restr 2.904 r_scangle_other 2.756 r_scbond_it 2.294 r_scbond_other 2.289 r_angle_refined_deg 2.189 r_mcangle_it 1.471 r_mcangle_other 1.467 r_mcbond_other 1.242 r_mcbond_it 1.238 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 258 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SHELXL refinement SHARP phasing