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Crystal structure of B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q)
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 80 mM acetic acid pH 3.6, 20 mM acetic acid pH 5.8, 30% 2,4-methylpentanediol, 200 mM NaCl and 20 mM zinc sulfate
Crystal Properties Matthews coefficient Solvent content 2.67 53.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.903 α = 90 b = 63.057 β = 103.31 c = 53.225 γ = 90
Symmetry Space Group P 1 21 1
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 2018-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.098 ALS 8.2.2
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 1.4 51.8 90.03 0.1 7.8 9.9 44547
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 1.398 1.434 25.89
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 1.4 40.06 44547 2317 90.03 0.11511 0.1129 0.1126 0.15813 0.157 RANDOM 19.862
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] 0.13 -0.4 -0.05 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.856 r_sphericity_free 31.361 r_sphericity_bonded 18.116 r_dihedral_angle_3_deg 13.618 r_dihedral_angle_4_deg 9.851 r_dihedral_angle_1_deg 5.961 r_long_range_B_refined 5.758 r_long_range_B_other 5.272 r_scangle_other 5.125 r_scbond_it 4.563
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.856 r_sphericity_free 31.361 r_sphericity_bonded 18.116 r_dihedral_angle_3_deg 13.618 r_dihedral_angle_4_deg 9.851 r_dihedral_angle_1_deg 5.961 r_long_range_B_refined 5.758 r_long_range_B_other 5.272 r_scangle_other 5.125 r_scbond_it 4.563 r_scbond_other 4.486 r_rigid_bond_restr 3.788 r_mcangle_it 2.747 r_mcangle_other 2.747 r_mcbond_it 2.182 r_mcbond_other 2.157 r_angle_refined_deg 1.85 r_angle_other_deg 1.059 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 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 1764 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing