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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 1 microliter of protein at 10 mg/mL in 20 mM sodium chloride was added to 1 microliter of 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 2.52 51.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.66 α = 90 b = 99.352 β = 97.4 c = 77.639 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 2.45 30 98.2 0.059 18.425 3.63 36017 36017
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 2.45 2.54 82.3 0.241 2.28
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1FP5 2.45 28.71 35946 35946 1824 98.75 0.23182 0.22936 0.27748 0.3053 RANDOM 31.781
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] 0.57 0.21 0.55 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28 r_dihedral_angle_4_deg 15.758 r_dihedral_angle_3_deg 14.975 r_dihedral_angle_1_deg 6.204 r_mcangle_it 2.569 r_scangle_it 2.179 r_mcbond_it 1.522 r_angle_refined_deg 1.448 r_scbond_it 1.396 r_angle_other_deg 0.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28 r_dihedral_angle_4_deg 15.758 r_dihedral_angle_3_deg 14.975 r_dihedral_angle_1_deg 6.204 r_mcangle_it 2.569 r_scangle_it 2.179 r_mcbond_it 1.522 r_angle_refined_deg 1.448 r_scbond_it 1.396 r_angle_other_deg 0.746 r_mcbond_other 0.277 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 6624 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement DENZO data reduction PDB_EXTRACT data extraction MAR345 data collection CNS phasing