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Structural Characterization of a Mutated, ADCC-Enhanced Human Fc Fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DTQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 298 8% PEG 3350, 200 mM Zn Acetate, 5% Glycerol, 0.1 M Imidazole -Malate buffer, pH 8.0, VAPOR DIFFUSION, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.68 54.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.869 α = 90 b = 147.492 β = 90 c = 74.315 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2007-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.53 47.25 92.6 0.159 0.159 7.5 3.1 8675 8675 36
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 2.53 2.59 100 0.614 0.614 1.9 3.1 924
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 2DTQ 2.534 47.25 8675 8264 398 91.42 0.23506 0.23215 0.2321 0.29287 0.2973 RANDOM 36.253
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] -2.66 -2.69 5.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.681 r_dihedral_angle_4_deg 22.242 r_dihedral_angle_3_deg 18.156 r_dihedral_angle_1_deg 7.564 r_scangle_it 3.03 r_angle_refined_deg 1.88 r_scbond_it 1.864 r_mcangle_it 1.136 r_mcbond_it 0.74 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.681 r_dihedral_angle_4_deg 22.242 r_dihedral_angle_3_deg 18.156 r_dihedral_angle_1_deg 7.564 r_scangle_it 3.03 r_angle_refined_deg 1.88 r_scbond_it 1.864 r_mcangle_it 1.136 r_mcbond_it 0.74 r_nbtor_refined 0.322 r_nbd_refined 0.238 r_symmetry_vdw_refined 0.224 r_xyhbond_nbd_refined 0.2 r_symmetry_hbond_refined 0.17 r_metal_ion_refined 0.133 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1675 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 114
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling