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Crystal structure of mutant Pro9Ser of scorpion alpha-like neurotoxin BmK M1 from Buthus martensii Karsch
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 4.6 293 Sodium phosphate, PEG400, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.907 α = 90 b = 46.907 β = 90 c = 53.748 γ = 120
Symmetry Space Group P 32 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 283 CCD ADSC QUANTUM 4 2000-11-20 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) R Sym 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 30 100 0.053 0.053 7.9 7 13889 13889 20.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.4 1.48 100 0.355 0.355 2 4.7 1988
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1SN1 1.4 19 13889 13889 1405 100 0.19494 0.19494 0.1924 0.21589 0.2331 RANDOM 15.27
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] -0.2 -0.1 -0.2 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.425 r_dihedral_angle_1_deg 4.658 r_scangle_it 4.106 r_scbond_it 2.794 r_mcangle_it 2.141 r_angle_refined_deg 1.669 r_mcbond_it 1.151 r_angle_other_deg 0.748 r_symmetry_vdw_refined 0.5 r_symmetry_vdw_other 0.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.425 r_dihedral_angle_1_deg 4.658 r_scangle_it 4.106 r_scbond_it 2.794 r_mcangle_it 2.141 r_angle_refined_deg 1.669 r_mcbond_it 1.151 r_angle_other_deg 0.748 r_symmetry_vdw_refined 0.5 r_symmetry_vdw_other 0.228 r_nbd_other 0.206 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.174 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 520 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing