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Structure of PR 10 Allergen Ara h 8.01 with Quercetin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 0.1 M BIS-TRIS pH 5.5, 2.0 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.47 50.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.938 α = 90 b = 52 β = 97.71 c = 55.62 γ = 90
Symmetry Space Group C 1 2 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 RAYONIX MX-300 2014-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.5 40 97.4 0.05 0.05 0.073 0.04 20.1 3.3 16565 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 100 0.577 0.577 0.677 0.371 2.3 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 4MAP 2.51 40 15747 814 96.72 0.23726 0.23532 0.2344 0.27278 0.2703 RANDOM 57.495
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] -0.01 3.6 -4.71 3.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.928 r_dihedral_angle_4_deg 17.914 r_dihedral_angle_3_deg 13.936 r_dihedral_angle_1_deg 6.378 r_long_range_B_refined 6.11 r_long_range_B_other 6.096 r_angle_other_deg 3.77 r_mcangle_it 3.189 r_mcangle_other 3.189 r_scangle_other 2.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.928 r_dihedral_angle_4_deg 17.914 r_dihedral_angle_3_deg 13.936 r_dihedral_angle_1_deg 6.378 r_long_range_B_refined 6.11 r_long_range_B_other 6.096 r_angle_other_deg 3.77 r_mcangle_it 3.189 r_mcangle_other 3.189 r_scangle_other 2.814 r_mcbond_it 1.848 r_mcbond_other 1.848 r_scbond_it 1.656 r_scbond_other 1.654 r_angle_refined_deg 1.643 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other 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 3497 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing HKL-3000 refinement