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Native Crystal Structure of the Type III Secretion chaperone SycT from Yersinia enterocolitica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BSH PDB ENTRIES 2BSH, 2BSI experimental model PDB 2BSI PDB ENTRIES 2BSH, 2BSI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.1 M SODIUM CITRATE PH 5.6, 5 % ISOPROPANOL, 21 % POLYETHYLENE GLYCOL 4000, HANGING-DROP VAPOR DIFFUSION AT 4 DEGREE CELSIUS
Crystal Properties Matthews coefficient Solvent content 2.26 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.112 α = 90 b = 79.562 β = 101.21 c = 52.093 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 MARRESEARCH 2004-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 MPG/DESY, HAMBURG BW6
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 1.83 79.5 97.6 0.06 14.8 5.6 23529 2
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 1.83 1.86 83.5 0.38 2.1 1.7
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 PDB ENTRIES 2BSH, 2BSI 1.83 79.56 22341 1185 97.5 0.186 0.184 0.1865 0.232 0.1861 RANDOM 28.1
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] 0.01 -0.74 -0.86 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.52 r_dihedral_angle_4_deg 24.915 r_dihedral_angle_3_deg 13.178 r_dihedral_angle_1_deg 5.961 r_scangle_it 3.56 r_scbond_it 2.411 r_mcangle_it 1.611 r_angle_refined_deg 1.484 r_mcbond_it 1.038 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.52 r_dihedral_angle_4_deg 24.915 r_dihedral_angle_3_deg 13.178 r_dihedral_angle_1_deg 5.961 r_scangle_it 3.56 r_scbond_it 2.411 r_mcangle_it 1.611 r_angle_refined_deg 1.484 r_mcbond_it 1.038 r_nbtor_refined 0.307 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.197 r_xyhbond_nbd_refined 0.151 r_symmetry_hbond_refined 0.135 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2060 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing