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Crystal structure of the N-terminal domain of the Legionella pneumophila protein SidC at 2.4A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other partial model after phasing and building in AutoSol
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.1M sodium cacodylate, 0.2M magnesium chloride, 10% PEG 1000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K 2 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.1M sodium citrate, 0.2M sodium acetate, 10% PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.055 α = 90 b = 119.055 β = 90 c = 201.7 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2010-10-06 M SINGLE WAVELENGTH 2 2 x-ray 100 PIXEL DECTRIS PILATUS 6M 2012-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9786 SLS X10SA 2 SYNCHROTRON SLS BEAMLINE X10SA 0.9794 SLS X10SA
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 2.4 50 99.8 0.101 0.054 19.03 28.65 124784 -3
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 2.4 2.5 99.8 0.579 0.473 2.87 28.32
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 partial model after phasing and building in AutoSol 2.4 45.9 124784 6240 100 0.2031 0.2 0.2014 0.2618 0.2611 RANDOM 50.024
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] -2.22 -1.11 -2.22 3.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.63 r_dihedral_angle_4_deg 17.201 r_dihedral_angle_3_deg 16.447 r_dihedral_angle_1_deg 6.764 r_scangle_it 3.974 r_scbond_it 2.436 r_angle_refined_deg 1.669 r_mcangle_it 1.512 r_angle_other_deg 0.978 r_mcbond_it 0.788
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.63 r_dihedral_angle_4_deg 17.201 r_dihedral_angle_3_deg 16.447 r_dihedral_angle_1_deg 6.764 r_scangle_it 3.974 r_scbond_it 2.436 r_angle_refined_deg 1.669 r_mcangle_it 1.512 r_angle_other_deg 0.978 r_mcbond_it 0.788 r_mcbond_other 0.173 r_chiral_restr 0.096 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19440 Nucleic Acid Atoms Solvent Atoms 419 Heterogen Atoms 123
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data scaling PHENIX phasing