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Crystal structure of SopD, a type III secreted virulence effector from Salmonella enterica
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7 295 0.1M HEPES pH 7, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.42 49.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.525 α = 90 b = 102.743 β = 105.53 c = 76.018 γ = 90
Symmetry Space Group P 1 21 1
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 MAR CCD 165 mm 2011-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 2.15 50 99 0.064 17.4 7.5 37360
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 2.15 2.23 100 0.521 7.6 3761
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.15 50 35455 1867 98.76 0.2138 0.2122 0.2132 0.2434 0.2429 RANDOM 55.801
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] 1.28 -0.64 -0.66 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.997 r_dihedral_angle_3_deg 19.842 r_dihedral_angle_4_deg 18.122 r_dihedral_angle_1_deg 7.046 r_scangle_it 4.895 r_scbond_it 3.239 r_mcangle_it 1.975 r_angle_refined_deg 1.969 r_mcbond_it 1.066 r_chiral_restr 0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.997 r_dihedral_angle_3_deg 19.842 r_dihedral_angle_4_deg 18.122 r_dihedral_angle_1_deg 7.046 r_scangle_it 4.895 r_scbond_it 3.239 r_mcangle_it 1.975 r_angle_refined_deg 1.969 r_mcbond_it 1.066 r_chiral_restr 0.141 r_bond_refined_d 0.023 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4473 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SHARP phasing