☰ Navigation Tabs
Depressant anti-insect neurotoxin, LqhIT2 from Leiurus quinquestriatus hebraeus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2SN3 PDB ENTRY 2SN3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 protein concentration 8mg/ml, precepitant 1.5 M LiSO4,
buffer 0.1 M NA, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.02 38.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 19.66 α = 90 b = 51.423 β = 107.75 c = 28.917 γ = 90
Symmetry Space Group P 1 21 1
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 QUANTUM 4 mirrors 2002-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 1.0052 ESRF ID14-4
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 1.2 50 94.7 0.038 0.038 43.63 3.1 16312 16312 -3 6.81
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) 1.2 1.22 90.5 0.046 0.046 22.77 2.1 773
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 2SN3 1.2 27.54 -3 16312 16246 830 94.68 0.097 0.097 0.096 0.12 0.1522 RANDOM 8.216
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] -0.35 -0.1 0.56 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.911 r_sphericity_free 13.164 r_dihedral_angle_3_deg 12.916 r_scangle_it 6.555 r_scbond_it 5.642 r_dihedral_angle_1_deg 5.479 r_sphericity_bonded 5.06 r_mcangle_it 3.741 r_mcbond_it 3.387 r_rigid_bond_restr 2.611
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.911 r_sphericity_free 13.164 r_dihedral_angle_3_deg 12.916 r_scangle_it 6.555 r_scbond_it 5.642 r_dihedral_angle_1_deg 5.479 r_sphericity_bonded 5.06 r_mcangle_it 3.741 r_mcbond_it 3.387 r_rigid_bond_restr 2.611 r_dihedral_angle_4_deg 2.314 r_angle_refined_deg 1.659 r_mcbond_other 1.526 r_angle_other_deg 0.927 r_symmetry_vdw_other 0.291 r_nbd_refined 0.262 r_symmetry_hbond_refined 0.248 r_xyhbond_nbd_refined 0.229 r_symmetry_vdw_refined 0.228 r_nbd_other 0.194 r_nbtor_refined 0.191 r_chiral_restr 0.121 r_symmetry_metal_ion_refined 0.11 r_metal_ion_refined 0.095 r_nbtor_other 0.086 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 501 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 27
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ProDC data collection HKL-2000 data reduction