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Structure of the major pilin protein (T-13) from Streptococcus pyogenes serotype GAS131465
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B2M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 291 20% w/v PEG 6000, 0.2 M MOPS pH 7.3
Crystal Properties Matthews coefficient Solvent content 3.05 59.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.772 α = 90 b = 114.968 β = 90 c = 128.711 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 210r 2014-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim 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 1.9 85.74 100 0.071 0.997 10.4 14.9 61489 17.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 100 0.762 0.461 1.2 14.9
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 3B2M 1.9 85.74 58361 3052 99.99 0.20519 0.2036 0.2119 0.23577 0.2406 RANDOM 28.679
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] -0.87 -0.01 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.98 r_dihedral_angle_3_deg 12.612 r_dihedral_angle_4_deg 11.285 r_long_range_B_refined 6.614 r_long_range_B_other 6.613 r_dihedral_angle_1_deg 6.49 r_scangle_other 3.291 r_mcangle_it 2.732 r_mcangle_other 2.732 r_scbond_it 2.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.98 r_dihedral_angle_3_deg 12.612 r_dihedral_angle_4_deg 11.285 r_long_range_B_refined 6.614 r_long_range_B_other 6.613 r_dihedral_angle_1_deg 6.49 r_scangle_other 3.291 r_mcangle_it 2.732 r_mcangle_other 2.732 r_scbond_it 2.001 r_scbond_other 1.999 r_mcbond_it 1.651 r_mcbond_other 1.649 r_angle_refined_deg 1.426 r_angle_other_deg 1.127 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4078 Nucleic Acid Atoms Solvent Atoms 411 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction