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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 2W1J PDB ENTRY 2W1J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 1.6 M magnesium sulfate, 0.1 M MES pH 6.5., VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.62 52.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.911 α = 90 b = 96.857 β = 90 c = 98.866 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 1.7 42.02 99.8 0.093 14.6 6.7 52404
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) 1.7 1.79 99.2 0.517 3.4 6.3 7580
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 2W1J 1.7 32.29 49719 2673 99.74 0.18958 0.18714 0.1876 0.23527 0.2344 5 % 23
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 38.25 r_dihedral_angle_4_deg 15.859 r_dihedral_angle_3_deg 13.643 r_dihedral_angle_1_deg 6.597 r_scangle_it 4.26 r_scbond_it 2.69 r_mcangle_it 1.948 r_angle_refined_deg 1.736 r_mcbond_it 1.162 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.25 r_dihedral_angle_4_deg 15.859 r_dihedral_angle_3_deg 13.643 r_dihedral_angle_1_deg 6.597 r_scangle_it 4.26 r_scbond_it 2.69 r_mcangle_it 1.948 r_angle_refined_deg 1.736 r_mcbond_it 1.162 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.211 r_nbd_refined 0.21 r_chiral_restr 0.203 r_xyhbond_nbd_refined 0.189 r_symmetry_vdw_refined 0.173 r_bond_refined_d 0.015 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3078 Nucleic Acid Atoms Solvent Atoms 557 Heterogen Atoms 24
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling