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Crystal structure of Taiwan cobra cardiotoxin A3 complexed with sulfogalactoceramide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H0J PDB ENTRY 1H0J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 1.8 M SODIUM MALONATE, 7.5% (V/V) TERT-BUTANOL, 7.5% (V/V) PENTAERYTHRITOL ETHOXYLATE (15/4 EO/OH), 0.08% (W/V) C10E6, 50 MM IMIDAZOLE, AND 50 MM TRIS-HCL, PH 7.0.
Crystal Properties Matthews coefficient Solvent content 2.6 52.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.327 α = 90 b = 63.327 β = 90 c = 120.879 γ = 120
Symmetry Space Group P 63 2 2
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 ADSC CCD MIRRORS 2004-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL17B2 NSRRC BL17B2
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 2.3 26.5 99.8 0.05 34.6 6.1 6821 2 25.9
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 2.3 2.4 100 0.34 5.1 5.8
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 THROUGHOUT PDB ENTRY 1H0J 2.31 26.47 2 6126 501 90 0.219 0.219 0.2387 0.222 0.2392 RANDOM 40.4
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] 2.31 3.08 2.31 -4.63
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.6 c_improper_angle_d 3.44 c_scangle_it 2.27 c_mcangle_it 1.94 c_angle_deg 1.7 c_scbond_it 1.59 c_mcbond_it 1.22 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.6 c_improper_angle_d 3.44 c_scangle_it 2.27 c_mcangle_it 1.94 c_angle_deg 1.7 c_scbond_it 1.59 c_mcbond_it 1.22 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 930 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 246
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing