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Structure of PR 10 Allergen Ara h 8.01 in complex with 3-Hydroxy-2-naphthoic acid
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 8.5 298 100 mM Tris, 25% PEG 3350, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.43 49.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.567 α = 90 b = 130.513 β = 90 c = 140.883 γ = 90
Symmetry Space Group P 21 21 21
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 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 2.3 40 99.8 0.043 0.043 0.051 0.018 45.7 8.1 37595 -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 2.3 2.34 100 0.314 0.314 0.445 0.155 4.75 8.3
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 2.3 40 35532 1900 99.78 0.22698 0.22521 0.2291 0.25995 0.2632 RANDOM 58.225
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] 2.58 -2.21 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.552 r_dihedral_angle_3_deg 14.05 r_dihedral_angle_4_deg 11.192 r_long_range_B_refined 7.893 r_dihedral_angle_1_deg 4.152 r_mcangle_it 3.727 r_scbond_it 2.36 r_mcbond_it 2.276 r_angle_refined_deg 1.714 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.552 r_dihedral_angle_3_deg 14.05 r_dihedral_angle_4_deg 11.192 r_long_range_B_refined 7.893 r_dihedral_angle_1_deg 4.152 r_mcangle_it 3.727 r_scbond_it 2.36 r_mcbond_it 2.276 r_angle_refined_deg 1.714 r_chiral_restr 0.092 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 5825 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 145
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing HKL-3000 refinement