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Crystal structure of the bacteriocin syringacin M from Pseudomonas syringae pv. tomato DC3000
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 7% w/v PEG 8000, 30% v/v ethylene glycol 0.03 M CaCl2, 0.03 M MgCl2, 5% dimethyl sulfoxide, 0.1 M Bicine/Tris base, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.687 α = 90 b = 159.687 β = 90 c = 100.173 γ = 120
Symmetry Space Group P 63 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 100 CCD ADSC QUANTUM 315r mirrors 2011-11-29 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795, 0.9796, 0.9253 Diamond I04
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 2.83 46.34 99.12 0.059 19.5 8.2 17330 17330 102.3
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 2.83 2.91 100 0.693 3.1 8.6 1337
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 2.83 46.34 17330 17330 929 99.12 0.20227 0.20227 0.2004 0.204 0.23914 0.2375 RANDOM 84.266
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] 1.03 0.52 1.03 -1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.497 r_dihedral_angle_3_deg 19.887 r_dihedral_angle_4_deg 15.32 r_dihedral_angle_1_deg 8.673 r_angle_refined_deg 2.028 r_angle_other_deg 1.096 r_chiral_restr 0.102 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.497 r_dihedral_angle_3_deg 19.887 r_dihedral_angle_4_deg 15.32 r_dihedral_angle_1_deg 8.673 r_angle_refined_deg 2.028 r_angle_other_deg 1.096 r_chiral_restr 0.102 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2083 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 5
Software Software Software Name Purpose EDNA data collection SHARP phasing REFMAC refinement XDS data reduction SCALA data scaling