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Structural Characterization of a Human Fc Fragment Engineered for Lack of Effector Functions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DTQ PDB entry 2DTQ, chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 298 5% PEG 3350, 200 mM Zn Acetate, 0.1 M Imidazole Malate, 5% Glycerol, pH 8.0, VAPOR DIFFUSION, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.74 55.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.178 α = 90 b = 147.301 β = 90 c = 75.473 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 100 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2007-06-26 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 2.3 30 98.3 0.062 0.062 13 4.3 12825 12617
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 2.3 2.38 90 0.3 0.3 3.3 2.7
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 2DTQ, chain A 2.3 30 12825 11994 619 98.43 0.21928 0.21637 0.2595 0.27541 0.2744 RANDOM 43.32
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] -3.83 0.96 2.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.844 r_dihedral_angle_4_deg 20.037 r_dihedral_angle_3_deg 17.124 r_dihedral_angle_1_deg 6.172 r_scangle_it 2.117 r_angle_refined_deg 1.482 r_scbond_it 1.312 r_mcangle_it 0.773 r_mcbond_it 0.502 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.844 r_dihedral_angle_4_deg 20.037 r_dihedral_angle_3_deg 17.124 r_dihedral_angle_1_deg 6.172 r_scangle_it 2.117 r_angle_refined_deg 1.482 r_scbond_it 1.312 r_mcangle_it 0.773 r_mcbond_it 0.502 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.267 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.168 r_symmetry_hbond_refined 0.166 r_chiral_restr 0.085 r_metal_ion_refined 0.013 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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_refined 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 1675 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction SCALEPACK data scaling PHASER phasing