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Modified single helix from the B-domain of protein A bound to IgG1 Fc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5U52
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 293 20% PEG 4000, 0.1M HEPES pH 7.2,
5mg/mL protein concentration.
Crystal Properties Matthews coefficient Solvent content 2.8 56.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.165 α = 90 b = 126.812 β = 90 c = 91.927 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 80 CCD MARMOSAIC 300 mm CCD 1997-05-15 M SINGLE WAVELENGTH 2 1 x-ray 80 CCD MARMOSAIC 300 mm CCD 1997-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.98 SSRL BL7-1 2 ROTATING ANODE RIGAKU RU300 1.0
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 1.7 41 96.4 0.074 29.8 5.7 29486 2 18.2
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 1.7 1.73 93.2 0.229 4.7 3.1
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 5U52 1.7 41.02 26544 2942 92.3 0.164 0.157 0.1703 0.227 0.2325 RANDOM 35.31
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] -0.83 0.36 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.35 r_sphericity_free 31.501 r_sphericity_bonded 25.131 r_dihedral_angle_4_deg 19.009 r_dihedral_angle_3_deg 13.807 r_long_range_B_refined 8.697 r_long_range_B_other 8.695 r_scangle_other 8.31 r_mcangle_it 7.425 r_mcangle_other 7.424
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.35 r_sphericity_free 31.501 r_sphericity_bonded 25.131 r_dihedral_angle_4_deg 19.009 r_dihedral_angle_3_deg 13.807 r_long_range_B_refined 8.697 r_long_range_B_other 8.695 r_scangle_other 8.31 r_mcangle_it 7.425 r_mcangle_other 7.424 r_scbond_other 6.968 r_scbond_it 6.967 r_dihedral_angle_1_deg 6.722 r_mcbond_it 5.954 r_mcbond_other 5.95 r_rigid_bond_restr 4.661 r_angle_other_deg 3.847 r_angle_refined_deg 1.964 r_chiral_restr 0.128 r_bond_refined_d 0.019 r_gen_planes_refined 0.014 r_gen_planes_other 0.003 r_bond_other_d 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1802 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing