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Crystal Structure of Major Birch Pollen Allergen Bet v 1 a in complex with naringenin.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A80 PDB ENTRY 4A80
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 pH 7
Crystal Properties Matthews coefficient Solvent content 1.96 37.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.65 α = 90 b = 55.42 β = 93.28 c = 37.89 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 225 mm CCD MIRRORS 2010-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.24 25.24 97.9 0.06 12.7 3.6 37419
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 1.24 1.31 88.4 0.17 5.2 2.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4A80 1.24 37.83 35510 1892 97.82 0.12826 0.1264 0.16238 0.1971 RANDOM 14.134
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] 0.5 -0.25 0.76 -1.29
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.156 r_dihedral_angle_2_deg 36.479 r_dihedral_angle_4_deg 31.394 r_sphericity_bonded 13.471 r_dihedral_angle_3_deg 12.535 r_scangle_it 6.338 r_dihedral_angle_1_deg 5.518 r_scbond_it 4.141 r_rigid_bond_restr 3.485 r_mcangle_it 3.186
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.156 r_dihedral_angle_2_deg 36.479 r_dihedral_angle_4_deg 31.394 r_sphericity_bonded 13.471 r_dihedral_angle_3_deg 12.535 r_scangle_it 6.338 r_dihedral_angle_1_deg 5.518 r_scbond_it 4.141 r_rigid_bond_restr 3.485 r_mcangle_it 3.186 r_mcbond_it 2.035 r_angle_refined_deg 1.698 r_angle_other_deg 0.926 r_symmetry_vdw_refined 0.293 r_nbd_refined 0.284 r_symmetry_vdw_other 0.238 r_nbd_other 0.204 r_xyhbond_nbd_refined 0.2 r_symmetry_hbond_refined 0.2 r_metal_ion_refined 0.198 r_nbtor_refined 0.188 r_chiral_restr 0.109 r_nbtor_other 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1225 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing