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BthTX-I, a svPLA2s-like toxin, complexed with zinc ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HZD PDB entry 3HZD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 Reservoir solution:
0.1 M TRIS HCl pH 8.5, 30% PEG4k and 0.1M LiSO4
Drop set up:
0.8 uL of protein (10.1 mg/mL), 0.09 uL of ZnCl2 (1 M), 0.32 uL of MnSO4 (12.5 mM) and 0.48 uL of reservoir solution 2 VAPOR DIFFUSION, HANGING DROP 8.5 293 Reservoir solution:
0.1 M TRIS HCl pH 8.5, 30% PEG4k and 0.1M LiSO4
Drop set up:
0.8 uL of protein (10.1 mg/mL), 0.09 uL of ZnCl2 (1 M), 0.32 uL of MnSO4 (12.5 mM) and 0.48 uL of reservoir solution
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.58 α = 90 b = 56.58 β = 90 c = 129.53 γ = 120
Symmetry Space Group P 31 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 80 CCD MAR CCD 165 mm 2011-09-15 M SINGLE WAVELENGTH 2 2 x-ray 80 CCD MARMOSAIC 225 mm CCD 2012-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.608 LNLS D03B-MX1 2 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.283 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.16 45.84 96.5 13.17 3.9 13020
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.16 2.28 99.6 2.02
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE PDB entry 3HZD 2.16 45.83 2.01 13016 651 96.56 0.1927 0.1905 0.1986 0.2339 0.2381 Random selection
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.439 f_angle_d 0.883 f_chiral_restr 0.032 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1853 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement