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Crystal structure of mature and fully active Der p 1 allergen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PCK PDB ID 7PCK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Low salt 4.5 277 25mM sodium acetate, pH 4.5, Low salt, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.46 50.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.12 α = 90 b = 78.43 β = 90 c = 83.774 γ = 90
Symmetry Space Group P 21 21 2
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 ADSC QUANTUM 210 channel-cut silicon monochromator, toroidally bent cylindrical grazing incidence mirror. Two monochromator crystals Si(311) cut and a lower resolution Si(111) cut. 2004-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.006768 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.85 50 98.3 0.117 0.1 34 36029 42045 -2 22.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.85 1.89 95.2 95.2 0.574 0.429 3 7.5 2476
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ID 7PCK 1.95 28.6 36177 34344 1832 98.42 0.191 0.18819 0.18492 0.1999 0.25171 0.1911 RANDOM 21.39
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] -2.31 3.73 -1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.2 r_dihedral_angle_4_deg 19.99 r_dihedral_angle_3_deg 16.975 r_dihedral_angle_1_deg 6.283 r_scangle_it 3.927 r_scbond_it 2.982 r_angle_refined_deg 1.999 r_mcbond_it 1.519 r_mcangle_it 1.399 r_angle_other_deg 1.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.2 r_dihedral_angle_4_deg 19.99 r_dihedral_angle_3_deg 16.975 r_dihedral_angle_1_deg 6.283 r_scangle_it 3.927 r_scbond_it 2.982 r_angle_refined_deg 1.999 r_mcbond_it 1.519 r_mcangle_it 1.399 r_angle_other_deg 1.192 r_symmetry_vdw_refined 0.519 r_chiral_restr 0.491 r_symmetry_vdw_other 0.424 r_symmetry_hbond_refined 0.384 r_nbd_refined 0.232 r_nbd_other 0.228 r_xyhbond_nbd_refined 0.214 r_nbtor_refined 0.183 r_mcbond_other 0.169 r_nbtor_other 0.095 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d 0.007 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3520 Nucleic Acid Atoms Solvent Atoms 791 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction