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Structure of the hypervariable region of Streptococcus pyogenes M3 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other low resolution model derived from SAD data
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 40% MPD
Crystal Properties Matthews coefficient Solvent content 2.11 41.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.474 α = 90 b = 24.107 β = 105.287 c = 78.007 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS3 6M 2019-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.969 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.918 75.25 99.7 0.058 0.9 14.8 6.2 21415
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.95 1.741 0.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.918 75.247 21411 1054 99.721 0.232 0.2297 0.2298 0.2679 0.2674 44.754
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] -0.913 -2.306 0.838 1.162
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.115 r_dihedral_angle_4_deg 24.143 r_dihedral_angle_3_deg 15.756 r_lrange_it 9.339 r_lrange_other 9.322 r_scangle_other 8.291 r_scangle_it 8.284 r_scbond_it 5.375 r_scbond_other 5.352 r_mcangle_it 4.957
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.115 r_dihedral_angle_4_deg 24.143 r_dihedral_angle_3_deg 15.756 r_lrange_it 9.339 r_lrange_other 9.322 r_scangle_other 8.291 r_scangle_it 8.284 r_scbond_it 5.375 r_scbond_other 5.352 r_mcangle_it 4.957 r_mcangle_other 4.955 r_dihedral_angle_1_deg 4.337 r_mcbond_it 3.936 r_mcbond_other 3.923 r_angle_other_deg 2.269 r_angle_refined_deg 1.44 r_symmetry_xyhbond_nbd_refined 0.224 r_nbd_refined 0.214 r_symmetry_nbd_other 0.198 r_xyhbond_nbd_refined 0.188 r_nbd_other 0.187 r_nbtor_refined 0.161 r_symmetry_nbd_refined 0.161 r_symmetry_xyhbond_nbd_other 0.095 r_chiral_restr 0.074 r_symmetry_nbtor_other 0.057 r_bond_other_d 0.035 r_bond_refined_d 0.009 r_gen_planes_other 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1787 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing