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Crystal Structure of Human IgG Fc Bearing Hybrid-type Glycans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AVE PDB ENTRY 3AVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 20% W/V PEG 3350 PH 5.5, 0.2 M SODIUM/POTASSIUM PHOSPHATE
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.041 α = 90 b = 72.991 β = 90 c = 140.833 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 77.2 CCD MARRESEARCH MIRRORS 2007-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.36 50 99.3 0.07 16.5 4.8 21447 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.36 2.44 98.7 0.47 2.4 4.5
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 PDB ENTRY 3AVE 2.36 39.51 20296 1083 99.26 0.21784 0.21535 0.2164 0.26613 0.2691 RANDOM 43.405
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] -3.39 -2.17 5.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.76 r_dihedral_angle_3_deg 15.04 r_dihedral_angle_4_deg 13.444 r_dihedral_angle_1_deg 5.706 r_angle_refined_deg 1.161 r_angle_other_deg 0.852 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.76 r_dihedral_angle_3_deg 15.04 r_dihedral_angle_4_deg 13.444 r_dihedral_angle_1_deg 5.706 r_angle_refined_deg 1.161 r_angle_other_deg 0.852 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3183 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing