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Cis/trans Isomerization of Non-prolyl Peptide Bond Observed in Crystal Structure of an Scorpion Toxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SN1 PDB entry 1SN1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 ammonium sulfate, Tris-HCl, Ethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.89 34.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.758 α = 90 b = 32.758 β = 90 c = 176.822 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 293 CCD ADSC QUANTUM 4 2000-12-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 1.0 Photon Factory BL-18B
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 1.4 29.3 85.8 0.04 19260
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) 1.4 1.48 74.6 0.201 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1SN1 1.4 29.49 19260 17355 1898 100 0.14416 0.14194 0.1425 0.16448 0.1675 RANDOM 15.774
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] 0.29 0.14 0.29 -0.43
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 9.308 r_dihedral_angle_1_deg 5.699 r_scangle_it 5.59 r_scbond_it 3.705 r_sphericity_bonded 3.416 r_mcangle_it 3.069 r_angle_refined_deg 1.986 r_rigid_bond_restr 1.901 r_mcbond_it 1.873 r_angle_other_deg 1.086
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 9.308 r_dihedral_angle_1_deg 5.699 r_scangle_it 5.59 r_scbond_it 3.705 r_sphericity_bonded 3.416 r_mcangle_it 3.069 r_angle_refined_deg 1.986 r_rigid_bond_restr 1.901 r_mcbond_it 1.873 r_angle_other_deg 1.086 r_symmetry_vdw_other 0.35 r_nbd_other 0.283 r_symmetry_vdw_refined 0.243 r_nbd_refined 0.229 r_symmetry_hbond_refined 0.159 r_chiral_restr 0.153 r_xyhbond_nbd_refined 0.141 r_nbtor_other 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_xyhbond_nbd_other r_symmetry_hbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1041 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling