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Structural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus agalactiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TVY PDB ENTRY 3TVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 15% PEG4000, 0.1 M Tris, pH 8.0, 0.2 M lithium sulfate, 10 mM cadmium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.34 63.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.585 α = 90 b = 124.585 β = 90 c = 117.839 γ = 120
Symmetry Space Group P 31 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 CCD ADSC QUANTUM 315 2011-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97949 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.619 39.788 100 0.096 21.9 7.3 32251
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.619 2.67 99.4 0.67 2 5.9
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 PDB ENTRY 3TVY 2.619 39.788 30583 1633 99.96 0.20836 0.20591 0.1995 0.25552 0.2446 RANDOM 56.557
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] 2.32 1.16 2.32 -3.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.419 r_dihedral_angle_4_deg 20.766 r_dihedral_angle_3_deg 18.569 r_dihedral_angle_1_deg 6.946 r_scangle_it 4.029 r_scbond_it 2.314 r_mcangle_it 1.684 r_angle_refined_deg 1.586 r_mcbond_it 0.89 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.419 r_dihedral_angle_4_deg 20.766 r_dihedral_angle_3_deg 18.569 r_dihedral_angle_1_deg 6.946 r_scangle_it 4.029 r_scbond_it 2.314 r_mcangle_it 1.684 r_angle_refined_deg 1.586 r_mcbond_it 0.89 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4610 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 9
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling