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Crystal structure of the complex of antibody and the allergen Bla g 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YG9 PDB entries 1YG9, 1MLB experimental model PDB 1MLB PDB entries 1YG9, 1MLB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 298 20% PEG 10000, 0.1M Ammonium sulfate, 5mM DTT, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.51 64.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.004 α = 90 b = 103.187 β = 94.83 c = 146.329 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 MARMOSAIC 300 mm CCD 2006-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 50 93.3 0.098 11.1 3.3 51667 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 65.2 0.301 2.2
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 entries 1YG9, 1MLB 2.81 50 49052 2610 92.82 0.23478 0.23238 0.2463 0.28058 0.2887 RANDOM 14.999
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] -0.39 -0.47 -1.33 1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.379 r_dihedral_angle_3_deg 16.615 r_dihedral_angle_4_deg 14.651 r_dihedral_angle_1_deg 6.442 r_angle_refined_deg 1.048 r_nbtor_refined 0.302 r_nbd_refined 0.234 r_symmetry_vdw_refined 0.167 r_xyhbond_nbd_refined 0.151 r_metal_ion_refined 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.379 r_dihedral_angle_3_deg 16.615 r_dihedral_angle_4_deg 14.651 r_dihedral_angle_1_deg 6.442 r_angle_refined_deg 1.048 r_nbtor_refined 0.302 r_nbd_refined 0.234 r_symmetry_vdw_refined 0.167 r_xyhbond_nbd_refined 0.151 r_metal_ion_refined 0.126 r_symmetry_hbond_refined 0.125 r_chiral_restr 0.072 r_bond_refined_d 0.006 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11600 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing