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Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, T16L, 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 18.5% PEG 400 0.1M HEPES pH 7.5
50 mM MgCl2, 5mM zinc sulfate
Crystal Properties Matthews coefficient Solvent content 2.36 47.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.828 α = 90 b = 69.828 β = 90 c = 24.157 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 1.5 34.94 97.72 0.1 7.8 9.9 8883
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 1.5 1.539 81.62
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 1.5 34.94 8883 443 97.72 0.13004 0.12806 0.16273 0.2008 RANDOM 30.314
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] -0.04 -0.04 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.559 r_dihedral_angle_3_deg 15.666 r_long_range_B_refined 7.001 r_long_range_B_other 6.685 r_scbond_other 6.509 r_scbond_it 6.492 r_scangle_other 6.145 r_dihedral_angle_1_deg 5.915 r_rigid_bond_restr 5.077 r_mcangle_it 4.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.559 r_dihedral_angle_3_deg 15.666 r_long_range_B_refined 7.001 r_long_range_B_other 6.685 r_scbond_other 6.509 r_scbond_it 6.492 r_scangle_other 6.145 r_dihedral_angle_1_deg 5.915 r_rigid_bond_restr 5.077 r_mcangle_it 4.34 r_mcangle_other 4.34 r_mcbond_it 3.331 r_mcbond_other 3.331 r_angle_refined_deg 1.848 r_angle_other_deg 1.577 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 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 440 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing