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Fc fragment of human IgG1 antibody, from NIST mAb
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D0S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 297 17% PEG 8K,
40 mM CaCl2
100 mM Na Hepes
Crystal Properties Matthews coefficient Solvent content 2.8 55.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.912 α = 90 b = 79.959 β = 90 c = 138.352 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 PIXEL DECTRIS PILATUS 6M 2015-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97934 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 30 94.4 0.098 7.2 6.7 30746
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.13 2.17 71 0.722
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 3d0s 2.116 12 29080 1477 94.18 0.20315 0.20105 0.24494 0.2599 RANDOM 56.627
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] -0.96 1.21 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.301 r_dihedral_angle_4_deg 20.929 r_dihedral_angle_3_deg 16.791 r_dihedral_angle_1_deg 6.976 r_long_range_B_refined 5.631 r_mcangle_it 1.795 r_angle_refined_deg 1.656 r_scbond_it 1.617 r_mcbond_it 1.15 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.301 r_dihedral_angle_4_deg 20.929 r_dihedral_angle_3_deg 16.791 r_dihedral_angle_1_deg 6.976 r_long_range_B_refined 5.631 r_mcangle_it 1.795 r_angle_refined_deg 1.656 r_scbond_it 1.617 r_mcbond_it 1.15 r_chiral_restr 0.101 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 3338 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 209
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling REFMAC phasing