2I61

Depressant anti-insect neurotoxin, LqhIT2 from Leiurus quinquestriatus hebraeus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2SN3PDB ENTRY 2SN3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5292protein 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 coefficientSolvent content
2.0238.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 19.66α = 90
b = 51.423β = 107.75
c = 28.917γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4mirrors2002-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-41.0052ESRFID14-4

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.25094.70.0380.03843.633.11631216312-36.81
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)RedundancyNumber Unique Reflections (All)
1.21.2290.50.0460.04622.772.1773

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2SN31.227.54-3163121624683094.680.0970.0970.0960.12RANDOM8.216
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]
-0.35-0.10.56-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.911
r_sphericity_free13.164
r_dihedral_angle_3_deg12.916
r_scangle_it6.555
r_scbond_it5.642
r_dihedral_angle_1_deg5.479
r_sphericity_bonded5.06
r_mcangle_it3.741
r_mcbond_it3.387
r_rigid_bond_restr2.611
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.911
r_sphericity_free13.164
r_dihedral_angle_3_deg12.916
r_scangle_it6.555
r_scbond_it5.642
r_dihedral_angle_1_deg5.479
r_sphericity_bonded5.06
r_mcangle_it3.741
r_mcbond_it3.387
r_rigid_bond_restr2.611
r_dihedral_angle_4_deg2.314
r_angle_refined_deg1.659
r_mcbond_other1.526
r_angle_other_deg0.927
r_symmetry_vdw_other0.291
r_nbd_refined0.262
r_symmetry_hbond_refined0.248
r_xyhbond_nbd_refined0.229
r_symmetry_vdw_refined0.228
r_nbd_other0.194
r_nbtor_refined0.191
r_chiral_restr0.121
r_symmetry_metal_ion_refined0.11
r_metal_ion_refined0.095
r_nbtor_other0.086
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms501
Nucleic Acid Atoms
Solvent Atoms90
Heterogen Atoms27

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ProDCdata collection
HKL-2000data reduction