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Structure of PR-10 Allergen Ara h 8.01.
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 298 56 mM sodium phosphate monobasic, 1.3 M monobasic potassium phosphate
Crystal Properties Matthews coefficient Solvent content 2.16 43.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.426 α = 90 b = 55.143 β = 91.32 c = 87.4 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 MX300-HS 2014-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 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 2.7 40 100 0.081 0.081 0.125 0.065 15.9 3.7 8130 -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) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75 100 0.507 0.507 0.705 0.362 0.782 2.1 3.7
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 4MAP 2.7 40 7623 397 99.93 0.21649 0.21354 0.27107 0.2415 RANDOM 52.348
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] 3.99 -0.19 -3.02 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.717 r_dihedral_angle_3_deg 13.993 r_dihedral_angle_4_deg 10.718 r_long_range_B_other 6.674 r_long_range_B_refined 6.673 r_dihedral_angle_1_deg 4.211 r_angle_other_deg 3.622 r_mcangle_it 2.966 r_mcangle_other 2.965 r_scangle_other 2.607
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.717 r_dihedral_angle_3_deg 13.993 r_dihedral_angle_4_deg 10.718 r_long_range_B_other 6.674 r_long_range_B_refined 6.673 r_dihedral_angle_1_deg 4.211 r_angle_other_deg 3.622 r_mcangle_it 2.966 r_mcangle_other 2.965 r_scangle_other 2.607 r_angle_refined_deg 1.808 r_mcbond_it 1.702 r_mcbond_other 1.697 r_scbond_it 1.498 r_scbond_other 1.495 r_chiral_restr 0.09 r_bond_refined_d 0.017 r_gen_planes_other 0.011 r_gen_planes_refined 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 2343 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing HKL-3000 refinement