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Crystal Structure of the Fucosylated Fc Fragment from Human Immunoglobulin G1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DTQ PDB ENTRY 2DTQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 7 277 deionized water, 20% 2,3-butanediol, pH 7.0, MICRODIALYSIS, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.78 55.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.419 α = 90 b = 78.471 β = 90 c = 143.758 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 RIGAKU JUPITER 210 2005-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32B2 1.0000 SPring-8 BL32B2
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 2 50 100 0.086 0.093 12.5 7 38712 38712 -3
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 2 2.11 100 0.677 0.73 3.3 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2DTQ 2 40.723 -3 38644 38644 1935 100 0.18757 0.18483 0.2102 0.23904 0.2467 RANDOM 41.11
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] -0.02 -0.04 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.25 r_dihedral_angle_4_deg 15.193 r_dihedral_angle_3_deg 14.782 r_dihedral_angle_1_deg 6.44 r_scangle_it 5.69 r_scbond_it 4.078 r_mcangle_it 2.868 r_mcbond_it 1.841 r_angle_refined_deg 1.672 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.25 r_dihedral_angle_4_deg 15.193 r_dihedral_angle_3_deg 14.782 r_dihedral_angle_1_deg 6.44 r_scangle_it 5.69 r_scbond_it 4.078 r_mcangle_it 2.868 r_mcbond_it 1.841 r_angle_refined_deg 1.672 r_nbtor_refined 0.313 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.157 r_symmetry_vdw_refined 0.146 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.103 r_symmetry_metal_ion_refined 0.029 r_bond_refined_d 0.017 r_metal_ion_refined 0.013 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3348 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 199
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling