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Structure of the type III effector/phosphothreonine lyase OspF from Shigella flexneri
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 10% isopropanol, 20% PEG4K, 1% PEG6K, 0.5% 2-methyl-2,4-pentanediol, 0.1 M HEPES pH 7.5. Cryoprotected in Paratone-N oil, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.125 α = 90 b = 62.125 β = 90 c = 239.586 γ = 90
Symmetry Space Group P 41 21 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 315 mirrors 2007-11-26 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD ADSC QUANTUM 315 2007-02-27 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-ID 2 SYNCHROTRON APS BEAMLINE 19-ID 0.97924, 0.97940 APS 19-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 2.7 50 99.8 0.057 48.01 13.1 13796 13771
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 2.7 2.8 100 0.426 7.14 13.6
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 MAD THROUGHOUT 2.7 43.94 13027 673 99.85 0.25158 0.24968 0.2464 0.28726 0.2902 RANDOM 71.02
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] 0.02 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.729 r_dihedral_angle_4_deg 23.59 r_dihedral_angle_3_deg 19.711 r_dihedral_angle_1_deg 6.818 r_scangle_it 1.732 r_angle_refined_deg 1.713 r_scbond_it 1.242 r_mcangle_it 0.652 r_mcbond_it 0.431 r_symmetry_hbond_refined 0.414
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.729 r_dihedral_angle_4_deg 23.59 r_dihedral_angle_3_deg 19.711 r_dihedral_angle_1_deg 6.818 r_scangle_it 1.732 r_angle_refined_deg 1.713 r_scbond_it 1.242 r_mcangle_it 0.652 r_mcbond_it 0.431 r_symmetry_hbond_refined 0.414 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.205 r_xyhbond_nbd_refined 0.175 r_nbd_refined 0.171 r_chiral_restr 0.113 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3193 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 8
Software Software Software Name Purpose HKL-3000 data collection SHELXS phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling