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Crystal structure of complex between recombinant Der p 2.0103 and Fab fragment of 7A1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KTJ 1KTJ, 3RVT experimental model PDB 3RVT 1KTJ, 3RVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 298 100 mM Bis-Tris, 200 mM ammonium acetate, 30-55% 2-methyl-2,4-pentanediol at pH 6.5 (well solution)
Crystal Properties Matthews coefficient Solvent content 2.75 55.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.094 α = 90 b = 43.336 β = 125.29 c = 105.935 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 2014-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 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 2.45 40 94.7 0.114 0.114 0.133 0.074 14.5 3 23826 -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 2.45 2.49 92.4 0.528 0.528 0.547 0.325 0.628 2.2 2.4
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 1KTJ, 3RVT 2.45 40 22564 1142 94.56 0.20583 0.20305 0.2063 0.26003 0.2621 RANDOM 42.886
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] -1.73 -0.79 3.61 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.21 r_dihedral_angle_4_deg 20.916 r_dihedral_angle_3_deg 12.673 r_dihedral_angle_1_deg 6.97 r_long_range_B_refined 4.509 r_long_range_B_other 4.419 r_angle_other_deg 3.904 r_mcangle_it 2.27 r_mcangle_other 2.27 r_scangle_other 1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.21 r_dihedral_angle_4_deg 20.916 r_dihedral_angle_3_deg 12.673 r_dihedral_angle_1_deg 6.97 r_long_range_B_refined 4.509 r_long_range_B_other 4.419 r_angle_other_deg 3.904 r_mcangle_it 2.27 r_mcangle_other 2.27 r_scangle_other 1.69 r_angle_refined_deg 1.436 r_mcbond_it 1.254 r_mcbond_other 1.254 r_scbond_it 0.972 r_scbond_other 0.969 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 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 4191 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing