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Crystal structure of de novo designed metal-controlled dimer of B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-zinc
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 4M NaCl 0.1M HEPES pH 7.5
50mM MgCl2, 5mM zinc sulfate
Crystal Properties Matthews coefficient Solvent content 3.17 61.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.155 α = 90 b = 63.155 β = 90 c = 39.61 γ = 90
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 ADSC QUANTUM 315r 2016-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0083 ALS 5.0.1
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 1.34 31.58 97.95 0.1 7.8 9.9 16453
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 1.34 1.374 83.64
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 MOLECULAR REPLACEMENT THROUGHOUT 1PGA 1.34 31.58 16453 849 97.95 0.10425 0.10425 0.12786 0.1642 RANDOM 25.219
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] 0.08 0.08 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.078 r_dihedral_angle_3_deg 15.017 r_long_range_B_refined 6.355 r_long_range_B_other 5.644 r_scangle_other 4.973 r_rigid_bond_restr 4.951 r_dihedral_angle_1_deg 4.926 r_scbond_it 4.866 r_scbond_other 4.857 r_mcangle_it 3.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.078 r_dihedral_angle_3_deg 15.017 r_long_range_B_refined 6.355 r_long_range_B_other 5.644 r_scangle_other 4.973 r_rigid_bond_restr 4.951 r_dihedral_angle_1_deg 4.926 r_scbond_it 4.866 r_scbond_other 4.857 r_mcangle_it 3.023 r_mcangle_other 3.018 r_mcbond_other 2.415 r_mcbond_it 2.41 r_angle_refined_deg 2.137 r_angle_other_deg 1.533 r_chiral_restr 0.114 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 439 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing