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Structure and activity of Streptococcus pyogenes SipA: a signal peptidase homologue essential for pilus polymerisation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K8W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 1M NaKPO4 pH 7.0, 8% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.66 66.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.811 α = 90 b = 132.811 β = 90 c = 107.156 γ = 120
Symmetry Space Group P 64 2 2
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 315 Adaptive and mechanically bent Si mirrors 2011-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95468 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 28.75 99.54 0.127 0.127 28.3 42.7 28860 28860 50.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.31 97.5 3.655 3.7 1.3 41.4 4006
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4K8W 2.2 28.75 27470 27299 1487 99.38 0.20231 0.20089 0.22933 0.1971 RANDOM 46.584
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] -0.03 -0.01 -0.03 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.359 r_dihedral_angle_3_deg 16.053 r_dihedral_angle_4_deg 15.053 r_dihedral_angle_1_deg 8.08 r_angle_refined_deg 1.559 r_angle_other_deg 0.782 r_chiral_restr 0.096 r_gen_planes_refined 0.016 r_bond_refined_d 0.011 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.359 r_dihedral_angle_3_deg 16.053 r_dihedral_angle_4_deg 15.053 r_dihedral_angle_1_deg 8.08 r_angle_refined_deg 1.559 r_angle_other_deg 0.782 r_chiral_restr 0.096 r_gen_planes_refined 0.016 r_bond_refined_d 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2158 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 49
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling