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Crystal structure of the IgE-Fc3-4 domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FP5 PDB entry 1FP5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.3 293 0.5 microliter of protein at 10 mg/mL in 20 mM sodium chloride was added to 0.5 microliter well solution (100 mM ammonium acetate, 100 mM sodium acetate pH 4.6, 30% (w/v) PEG 4000) and mixed by pipetting., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.56 51.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.9 α = 90 b = 104.9 β = 96.2 c = 150 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 113 CCD MAR CCD 130 mm 1999-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 1.0001 APS 5ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 30 99.9 0.073 16.7 3.7 37208 37208
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 100 0.541 3.4
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 (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 entry 1FP5 2.8 29.83 36905 36845 1860 100 0.24339 0.24144 0.2548 0.28015 0.2946 RANDOM 63.102
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 -0.56 1.53 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.105 r_dihedral_angle_3_deg 12.064 r_dihedral_angle_4_deg 10.085 r_dihedral_angle_1_deg 4.339 r_mcangle_it 1.182 r_angle_refined_deg 0.908 r_scangle_it 0.816 r_mcbond_it 0.672 r_angle_other_deg 0.616 r_scbond_it 0.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.105 r_dihedral_angle_3_deg 12.064 r_dihedral_angle_4_deg 10.085 r_dihedral_angle_1_deg 4.339 r_mcangle_it 1.182 r_angle_refined_deg 0.908 r_scangle_it 0.816 r_mcbond_it 0.672 r_angle_other_deg 0.616 r_scbond_it 0.477 r_mcbond_other 0.071 r_chiral_restr 0.053 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9910 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 366
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement DENZO data reduction PDB_EXTRACT data extraction MAR345 data collection CNS phasing