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Structure of the hypervariable region of Streptococcus pyogenes M3 protein in complex with a collagen peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other native M3 structure obtained through experimental phasing (about to be released)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100mM Tris pH8.5, 8% PEG10k
protein 1:1.5 peptide
Crystal Properties Matthews coefficient Solvent content 2.11 41.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.832 α = 87.326 b = 51.503 β = 84.78 c = 80.186 γ = 89.394
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 EIGER2 XE 16M 2019-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.970 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.32 79.77 90.2 1 2.1 1.8 35250
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.32 2.34 0.3
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 2.324 79.769 19530 947 89.595 0.243 0.2412 0.2438 0.2853 0.2825 40.861
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] -0.565 0.43 -0.858 0.796 0.149 -0.358
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.187 r_dihedral_angle_4_deg 24.104 r_dihedral_angle_3_deg 16.857 r_lrange_it 7.01 r_lrange_other 7.009 r_scangle_it 5.457 r_scangle_other 5.456 r_dihedral_angle_1_deg 5.111 r_mcangle_it 4.4 r_mcangle_other 4.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.187 r_dihedral_angle_4_deg 24.104 r_dihedral_angle_3_deg 16.857 r_lrange_it 7.01 r_lrange_other 7.009 r_scangle_it 5.457 r_scangle_other 5.456 r_dihedral_angle_1_deg 5.111 r_mcangle_it 4.4 r_mcangle_other 4.4 r_scbond_it 3.491 r_scbond_other 3.49 r_mcbond_it 2.898 r_mcbond_other 2.898 r_angle_refined_deg 1.253 r_angle_other_deg 1.17 r_symmetry_nbd_refined 0.302 r_nbd_other 0.262 r_nbd_refined 0.193 r_symmetry_nbd_other 0.171 r_xyhbond_nbd_refined 0.157 r_nbtor_refined 0.15 r_symmetry_xyhbond_nbd_refined 0.125 r_ncsr_local_group_1 0.115 r_ncsr_local_group_4 0.111 r_ncsr_local_group_3 0.109 r_ncsr_local_group_19 0.106 r_ncsr_local_group_8 0.105 r_ncsr_local_group_12 0.104 r_ncsr_local_group_20 0.098 r_ncsr_local_group_5 0.097 r_ncsr_local_group_15 0.095 r_ncsr_local_group_2 0.094 r_ncsr_local_group_18 0.094 r_symmetry_nbtor_other 0.089 r_ncsr_local_group_6 0.073 r_ncsr_local_group_9 0.066 r_ncsr_local_group_7 0.064 r_ncsr_local_group_16 0.063 r_ncsr_local_group_10 0.053 r_chiral_restr 0.049 r_ncsr_local_group_11 0.044 r_ncsr_local_group_17 0.044 r_ncsr_local_group_21 0.043 r_ncsr_local_group_13 0.042 r_ncsr_local_group_14 0.011 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4011 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing