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Crystal structure of the platelet activator convulxin, a disulfide linked a4b4 cyclic tetramer from the venom of Crotalus durissus terrificus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C3A PDB ENTRY 1C3A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 pH 4.60
Crystal Properties Matthews coefficient Solvent content 4.8 73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.906 α = 90 b = 131.906 β = 90 c = 112.849 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
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 2.4 30 97.6 0.061 12.1 2.4 36900 2
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 2.4 2.6 98.8 0.404 1.9
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 PDB ENTRY 1C3A 2.4 30 34998 1845 97.6 0.19 0.187 0.1965 0.264 0.267 RANDOM 47.25
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] 1.16 1.16 -2.33
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 8.456 r_dihedral_angle_1_deg 8.429 r_scbond_it 7.103 r_mcangle_it 6.529 r_mcbond_it 4.971 r_angle_refined_deg 2.693 r_symmetry_vdw_refined 0.447 r_nbd_refined 0.256 r_xyhbond_nbd_refined 0.212 r_chiral_restr 0.207
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 8.456 r_dihedral_angle_1_deg 8.429 r_scbond_it 7.103 r_mcangle_it 6.529 r_mcbond_it 4.971 r_angle_refined_deg 2.693 r_symmetry_vdw_refined 0.447 r_nbd_refined 0.256 r_xyhbond_nbd_refined 0.212 r_chiral_restr 0.207 r_symmetry_hbond_refined 0.194 r_bond_refined_d 0.033 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4318 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing