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Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-apo
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PGA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 31% PEG 4,000 0.1M Tris pH 8.5
200mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.18 43.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.892 α = 90 b = 42.892 β = 90 c = 102.168 γ = 120
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++ 2016-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 37.15 85.96 0.1 7.8 9.9 7581
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.304 2.363 20.11
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 1PGA 2.3 37.15 7581 416 85.96 0.19156 0.18784 0.1985 0.25762 0.2587 RANDOM 41.79
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] -5.62 -5.62 11.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.087 r_dihedral_angle_3_deg 19.418 r_dihedral_angle_1_deg 9.586 r_long_range_B_refined 6.039 r_long_range_B_other 5.577 r_mcangle_it 2.481 r_mcangle_other 2.48 r_angle_refined_deg 2.246 r_scangle_other 1.987 r_mcbond_it 1.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.087 r_dihedral_angle_3_deg 19.418 r_dihedral_angle_1_deg 9.586 r_long_range_B_refined 6.039 r_long_range_B_other 5.577 r_mcangle_it 2.481 r_mcangle_other 2.48 r_angle_refined_deg 2.246 r_scangle_other 1.987 r_mcbond_it 1.409 r_mcbond_other 1.407 r_scbond_it 1.146 r_scbond_other 1.146 r_angle_other_deg 1.126 r_chiral_restr 0.113 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_4_deg 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1756 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing