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Crystal structure of the major allergen from fire ant venom, Sol i 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QNX PDB ENTRY 1QNX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 THE HANGING-DROP VAPOR WATER (9.9 MG/ML) WAS MIXED WITH RESERVOIR SOLUTION (19% (W/V) POLYETHYLENE GLYCOL (PEG) 1000, 100 MM TRIS-HCL, PH 8.5) AT A RATIO OF 1:1.
Crystal Properties Matthews coefficient Solvent content 3.77 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.355 α = 90 b = 93.355 β = 90 c = 144.051 γ = 120
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 MARRESEARCH 2007-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 3.04 80.85 96.6 0.1 9.07 2.68 13121
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 3.04 3.07 96.6 0.4 1.37 2.52
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 1QNX 3.05 30 13061 652 96.3 0.203 0.201 0.2081 0.239 0.2434 RANDOM 47.89
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] 0.163 0.082 0.163 -0.245
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.234 r_dihedral_angle_4_deg 22.279 r_dihedral_angle_3_deg 16.365 r_dihedral_angle_1_deg 6.196 r_scangle_it 2.311 r_scbond_it 1.559 r_mcangle_it 1.029 r_angle_refined_deg 1.016 r_mcbond_it 0.692 r_symmetry_vdw_refined 0.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.234 r_dihedral_angle_4_deg 22.279 r_dihedral_angle_3_deg 16.365 r_dihedral_angle_1_deg 6.196 r_scangle_it 2.311 r_scbond_it 1.559 r_mcangle_it 1.029 r_angle_refined_deg 1.016 r_mcbond_it 0.692 r_symmetry_vdw_refined 0.247 r_nbd_refined 0.208 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.115 r_symmetry_hbond_refined 0.115 r_chiral_restr 0.062 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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 3219 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing