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Structure of PR-10 Allergen Ara h 8.01 in complex with epicatechin
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 295 150 mM potassium bromide, 30% PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.11 41.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.435 α = 90 b = 92.068 β = 91.79 c = 39.489 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 2013-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 1 APS 21-ID-G
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 50 99.9 0.063 0.063 0.074 0.036 29.8 4.1 9891 -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 0.333 0.333 0.423 0.205 3.9 4.2
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 4MAP 2.5 46.03 9231 557 99.93 0.22796 0.22531 0.2256 0.26855 0.2549 RANDOM 52.601
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] 1.26 -1.72 -2.79 1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.166 r_dihedral_angle_4_deg 26.821 r_dihedral_angle_3_deg 14.813 r_dihedral_angle_1_deg 5.365 r_long_range_B_refined 4.375 r_long_range_B_other 4.375 r_angle_other_deg 3.754 r_scangle_other 2.148 r_mcangle_it 2.123 r_mcangle_other 2.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.166 r_dihedral_angle_4_deg 26.821 r_dihedral_angle_3_deg 14.813 r_dihedral_angle_1_deg 5.365 r_long_range_B_refined 4.375 r_long_range_B_other 4.375 r_angle_other_deg 3.754 r_scangle_other 2.148 r_mcangle_it 2.123 r_mcangle_other 2.123 r_angle_refined_deg 1.714 r_scbond_it 1.306 r_scbond_other 1.305 r_mcbond_it 1.294 r_mcbond_other 1.293 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_other 0.009 r_gen_planes_refined 0.008 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 2328 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing HKL-3000 data processing