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Crystal structure of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, 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 70 mM acetic Acid pH 3.6, 30 mM acetic acid pH 5.8, 30% 2,4-methylpentanediol, 100 mM NaCl, and 20 mM zinc sulfate
Crystal Properties Matthews coefficient Solvent content 2.21 44.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.292 α = 90 b = 48.292 β = 90 c = 83.341 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 PIXEL DECTRIS PILATUS 6M-F 2012-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.00002 APS 24-ID-C
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 37.38 95.7 0.1 7.8 9.9 42380
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 1.4 1.44 70.44 0.29 6.5
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 37.38 38948 2082 95.66 0.14859 0.14499 0.1492 0.21447 0.2118 RANDOM 17.271
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] -0.41 -0.41 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.997 r_sphericity_free 25.224 r_dihedral_angle_3_deg 17.992 r_sphericity_bonded 11.471 r_dihedral_angle_4_deg 8.928 r_dihedral_angle_1_deg 6.738 r_rigid_bond_restr 5.592 r_long_range_B_refined 5.565 r_long_range_B_other 5.426 r_scangle_other 4.798
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.997 r_sphericity_free 25.224 r_dihedral_angle_3_deg 17.992 r_sphericity_bonded 11.471 r_dihedral_angle_4_deg 8.928 r_dihedral_angle_1_deg 6.738 r_rigid_bond_restr 5.592 r_long_range_B_refined 5.565 r_long_range_B_other 5.426 r_scangle_other 4.798 r_scbond_it 4.739 r_scbond_other 4.729 r_mcangle_it 3.629 r_mcangle_other 3.627 r_mcbond_other 3.187 r_mcbond_it 3.186 r_angle_refined_deg 3.177 r_angle_other_deg 1.699 r_chiral_restr 0.185 r_bond_refined_d 0.037 r_gen_planes_refined 0.019 r_gen_planes_other 0.007 r_bond_other_d 0.004 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 1792 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing