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Structure of PR 10 Allergen 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 6.5 298 200 mM NaCl, 100 mM Bis-Tris pH 6.5, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.4 48.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.451 α = 90 b = 62.507 β = 90 c = 186.585 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 MX-225 2013-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1 APS 19-BM
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 98.4 0.05 0.05 0.071 0.026 36.1 7.4 29305 -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 83.3 0.468 0.468 0.66 0.281 2.4 4.7
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-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 27787 1447 98.43 0.21683 0.21502 0.2209 0.25156 0.2553 RANDOM 67.317
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] 0.46 -2.2 1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.744 r_dihedral_angle_4_deg 30.302 r_dihedral_angle_3_deg 12.869 r_long_range_B_refined 9.106 r_dihedral_angle_1_deg 4.304 r_mcangle_it 3.852 r_scbond_it 3.15 r_mcbond_it 2.391 r_angle_refined_deg 1.773 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.744 r_dihedral_angle_4_deg 30.302 r_dihedral_angle_3_deg 12.869 r_long_range_B_refined 9.106 r_dihedral_angle_1_deg 4.304 r_mcangle_it 3.852 r_scbond_it 3.15 r_mcbond_it 2.391 r_angle_refined_deg 1.773 r_chiral_restr 0.093 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 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 4688 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement MOLREP phasing HKL-2000 data scaling HKL-3000 refinement