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Crystal structure of Beta-Cardiotoxin, a novel three-finger cardiotoxin from the venom of Ophiophagus hannah
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KXI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 vapour diffusion, hanging drop 7 298 25% (w/v) PEG 1500, Spermidine additive, pH 7, vapour diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.52 51.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.949 α = 90 b = 58.949 β = 90 c = 53.026 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 100 CCD Bruker AXIOM 200 2009-11-18 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 2.41 50.01 99.6 0.137 5.6 11.1 7999
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 2.41 2.5 96 0.484 8.9 784
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 1KXI 2.41 50 7983 787 99.63 0.2373 0.234 0.2336 0.2666 0.279 RANDOM 45.967
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] -9.93 -9.93 19.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.775 r_dihedral_angle_3_deg 22.531 r_dihedral_angle_4_deg 20.035 r_dihedral_angle_1_deg 8.675 r_scangle_it 3.712 r_scbond_it 2.146 r_mcangle_it 2.123 r_angle_refined_deg 1.896 r_mcbond_it 1.169 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.775 r_dihedral_angle_3_deg 22.531 r_dihedral_angle_4_deg 20.035 r_dihedral_angle_1_deg 8.675 r_scangle_it 3.712 r_scbond_it 2.146 r_mcangle_it 2.123 r_angle_refined_deg 1.896 r_mcbond_it 1.169 r_chiral_restr 0.111 r_bond_refined_d 0.016 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1293 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling