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Crystal structure of the Yersinia Pestis type III secretion chaperone SycH in complex with a stable fragment of YscM2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.6 298 1.8 M ammonium sulphate, 200 mM magnesium acetate, 100 mM CAPSO, 2% dioxane, 1.6 mM CHAPS, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.2 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.664 α = 90 b = 63.664 β = 90 c = 162.263 γ = 120
Symmetry Space Group P 61 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 MARRESEARCH 2003-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.98397 APS 22-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 2.38 25 85 0.069 26.9 13 9196 7916 2 2 66.026
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 2.38 2.48 67.5 0.45 4 10 888
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MIR THROUGHOUT 2.38 25 2 2 9196 7916 388 98.83 0.24541 0.24312 0.2573 0.29219 0.2487 RANDOM 67.69
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] 0.61 0.3 0.61 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 11.704 r_scangle_it 7.128 r_scbond_it 4.59 r_angle_refined_deg 3.518 r_mcangle_it 3.376 r_mcbond_it 1.897 r_angle_other_deg 1.484 r_symmetry_hbond_refined 0.514 r_nbd_refined 0.285 r_symmetry_vdw_other 0.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 11.704 r_scangle_it 7.128 r_scbond_it 4.59 r_angle_refined_deg 3.518 r_mcangle_it 3.376 r_mcbond_it 1.897 r_angle_other_deg 1.484 r_symmetry_hbond_refined 0.514 r_nbd_refined 0.285 r_symmetry_vdw_other 0.284 r_nbd_other 0.278 r_xyhbond_nbd_refined 0.276 r_symmetry_vdw_refined 0.259 r_chiral_restr 0.193 r_nbtor_other 0.128 r_bond_refined_d 0.044 r_gen_planes_refined 0.016 r_gen_planes_other 0.012 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 993 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling SOLVE phasing