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Cross-reactivity and crystal structure of Malassezia sympodialis Thioredoxin (Mala s 13), a member of a new pan-allergen family
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EP7 PDB ENTRY 1EP7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 1.8 M AMMONIUM SULFATE, 3% PEG400, 0.1 M IMIDAZOLE PH 7
Crystal Properties Matthews coefficient Solvent content 1.91 35.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.496 α = 90 b = 51.986 β = 99.49 c = 53.023 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 MARRESEARCH 2004-05-05 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 1.41 37 99.6 0.04 18.9 4.4 38712 -3
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 1.41 1.43 93.2 0.25 3.4
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 1EP7 1.41 37 36757 1938 99.6 0.141 0.14 0.153 0.168 0.1764 RANDOM 15.77
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] -0.4 -0.08 0.32 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.899 r_dihedral_angle_3_deg 9.835 r_scangle_it 7.372 r_scbond_it 5.664 r_dihedral_angle_4_deg 4.231 r_dihedral_angle_1_deg 4.025 r_mcangle_it 3.995 r_mcbond_it 3.267 r_angle_refined_deg 1.445 r_angle_other_deg 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.899 r_dihedral_angle_3_deg 9.835 r_scangle_it 7.372 r_scbond_it 5.664 r_dihedral_angle_4_deg 4.231 r_dihedral_angle_1_deg 4.025 r_mcangle_it 3.995 r_mcbond_it 3.267 r_angle_refined_deg 1.445 r_angle_other_deg 0.78 r_nbd_refined 0.248 r_symmetry_vdw_other 0.211 r_nbtor_refined 0.178 r_nbd_other 0.168 r_xyhbond_nbd_refined 0.156 r_symmetry_vdw_refined 0.154 r_nbtor_other 0.085 r_symmetry_hbond_refined 0.08 r_chiral_restr 0.061 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 1759 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing