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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 7.5 295 20% PEG3000, 0.1 M HEPES, 0.2 M NaCl, 10 mM Spermine-4HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.14 42.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.071 α = 74.12 b = 77.26 β = 87.25 c = 96.402 γ = 89.99
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2010-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2 46.304 89 0.07 11.5 3.6 88454
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 2 2.07 80.2 0.29 4.2 3.7
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 46.304 84024 4418 88.97 0.19987 0.19826 0.1976 0.23068 0.2301 RANDOM 24.932
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] -0.35 -0.05 0.16 0.32 0.07 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.996 r_dihedral_angle_4_deg 18.257 r_dihedral_angle_3_deg 16.092 r_dihedral_angle_1_deg 6.597 r_scangle_it 3.383 r_scbond_it 2.119 r_angle_refined_deg 1.465 r_mcangle_it 1.374 r_mcbond_it 0.766 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.996 r_dihedral_angle_4_deg 18.257 r_dihedral_angle_3_deg 16.092 r_dihedral_angle_1_deg 6.597 r_scangle_it 3.383 r_scbond_it 2.119 r_angle_refined_deg 1.465 r_mcangle_it 1.374 r_mcbond_it 0.766 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11380 Nucleic Acid Atoms Solvent Atoms 759 Heterogen Atoms 20
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling