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The crystal structure of Streptococcus pneumoniae Sortase C provides novel insights into catalysis as well as pilin substrate specificity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G66 PDB ENTRY 3G66
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 0.1 M MES pH 7.0 and 1.9 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.59 52.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.578 α = 90 b = 96.554 β = 90 c = 98.818 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 100 CCD ADSC QUANTUM 210 2008-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 49.39 99.2 0.011 16.1 7.2 31946 18.9
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) 2 2.11 97.2 0.305 6.3 6.3 4490
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 3G66 2 43.6 30362 1620 99.23 0.19568 0.19228 0.1925 0.25812 0.2568 5% 25.036
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.841 r_dihedral_angle_3_deg 16.411 r_dihedral_angle_4_deg 15.487 r_dihedral_angle_1_deg 6.529 r_scangle_it 4.725 r_scbond_it 3.265 r_mcangle_it 2.176 r_angle_refined_deg 2.132 r_mcbond_it 1.401 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.841 r_dihedral_angle_3_deg 16.411 r_dihedral_angle_4_deg 15.487 r_dihedral_angle_1_deg 6.529 r_scangle_it 4.725 r_scbond_it 3.265 r_mcangle_it 2.176 r_angle_refined_deg 2.132 r_mcbond_it 1.401 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.258 r_symmetry_hbond_refined 0.251 r_nbd_refined 0.24 r_chiral_restr 0.226 r_xyhbond_nbd_refined 0.192 r_bond_refined_d 0.023 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3076 Nucleic Acid Atoms Solvent Atoms 467 Heterogen Atoms 34
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling