☰ Navigation Tabs
Crystal Structure of the Defucosylated Fc Fragment from Human Immunoglobulin G1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H3X PDB ENTRY 1H3X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 7 277 Deionized water, pH 7.0, MICRODIALYSIS, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.74 55.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.472 α = 90 b = 77.69 β = 90 c = 143.462 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 2.2 50 98.9 0.08 0.091 10.2 4.7 28426 28426 -3 42.361
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 2.32 99.7 0.669 0.753 2.6 4.8 4116
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 (All) 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 1H3X 2.2 50 -3 28378 26944 1434 98.26 0.19483 0.19483 0.19195 0.2062 0.25064 0.2595 RANDOM 37.021
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] -3.25 -0.4 3.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.701 r_dihedral_angle_4_deg 21.168 r_dihedral_angle_3_deg 18.103 r_dihedral_angle_1_deg 7.874 r_scangle_it 4.747 r_scbond_it 3.429 r_angle_refined_deg 2.593 r_mcangle_it 2.079 r_mcbond_it 1.688 r_angle_other_deg 1.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.701 r_dihedral_angle_4_deg 21.168 r_dihedral_angle_3_deg 18.103 r_dihedral_angle_1_deg 7.874 r_scangle_it 4.747 r_scbond_it 3.429 r_angle_refined_deg 2.593 r_mcangle_it 2.079 r_mcbond_it 1.688 r_angle_other_deg 1.104 r_symmetry_vdw_refined 0.511 r_mcbond_other 0.424 r_symmetry_vdw_other 0.302 r_nbd_refined 0.243 r_symmetry_hbond_refined 0.228 r_nbd_other 0.206 r_nbtor_refined 0.195 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.156 r_nbtor_other 0.105 r_bond_refined_d 0.033 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 3348 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing