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Crystal Structure of STM2138, a novel virulence chaperone in Salmonella
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K3E PDB entry 1K3E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 100 mM Bis-Tris propane, 200 mM MgCl2, 35% PEG 3350,
3.95 mM FOS-choline-9, 5% (v/v) Jeffamine M-600, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.27 45.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.838 α = 90 b = 46.832 β = 106.39 c = 65.936 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 210 toroidal mirror 2008-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 1.1000 NSLS X12C
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 2.49 50 98.5 0.064 13.5 3.62 10664 10664 1 1 54.8
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 2.49 2.58 94.6 0.316 3.4 3.58
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 PDB entry 1K3E 2.5 33.4 1 1 10170 10170 538 99.91 0.21635 0.21448 0.2127 0.25256 0.2518 RANDOM 63.824
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] -2.16 1.66 -0.98 4.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.567 r_dihedral_angle_3_deg 16.972 r_dihedral_angle_4_deg 14.049 r_scangle_it 7.418 r_dihedral_angle_1_deg 6.073 r_scbond_it 5.029 r_mcangle_it 4.111 r_mcbond_it 2.323 r_angle_refined_deg 1.371 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.567 r_dihedral_angle_3_deg 16.972 r_dihedral_angle_4_deg 14.049 r_scangle_it 7.418 r_dihedral_angle_1_deg 6.073 r_scbond_it 5.029 r_mcangle_it 4.111 r_mcbond_it 2.323 r_angle_refined_deg 1.371 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.243 r_nbd_refined 0.224 r_symmetry_hbond_refined 0.221 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2174 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms
Software Software Software Name Purpose CBASS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling