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Crystal structure of the cytoplasmic domain of Spa40, the specificity switch for the Shigella flexneri Type III Secretion System
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BZL PDB ENTRY 3BZL WITH SIDECHAINS MUTATED TO SER
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 SITTING DROPS CONTAINING 200 NL PROTEIN (3.3 MG/ML IN 20 MM TRIS PH 8.0, 500 MM NACL) AND 200 NL RESERVOIR SOLUTION (0.1M HEPES PH7.0, 0.2M NH4CL AND 20% PEG W/V 6000) WERE EQUILIBRATED AGAINST 100 UL RESERVOIRS AT 20 C. CRYSTALS WERE CRYOPROTECTED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 25% (V/V) GLYCEROL. THE ASYMMETRIC UNIT VOLUME IS NOT SUFFICIENT TO ACCOMMODATE THE ENTIRE SPA40 CONSTRUCT. WE ASSUME THAT THE PROTEIN HAS UNDERGONE SOME PROTEOLYSIS ADDITIONAL TO THE SELF-CLEAVAGE BETWEEN RESIDUES 257 AND 258, REMOVING EITHER THE DISORDERED N-TERMINUS OR THE C-TERMINAL HIS TAG. THE SOLVENT CONTENT QUOTED IS FOR RESIDUE 237 TO THE END OF THE CONSTRUCT.
Crystal Properties Matthews coefficient Solvent content 1.67 26.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.035 α = 102.52 b = 30.753 β = 110.97 c = 32.099 γ = 94.3
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 CCD MIRRORS 2008-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 30 93.2 0.11 3.8 2.6 5433 -3 21.6
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 2.05 93.3 0.4 1.7 2.7
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 ENTRY 3BZL WITH SIDECHAINS MUTATED TO SER 2 29.59 5181 252 93.2 0.18 0.178 0.1834 0.227 0.2357 RANDOM 18.59
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] -1.29 -0.4 -1.06 1.11 0.92 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.309 r_dihedral_angle_3_deg 15.846 r_dihedral_angle_4_deg 13.76 r_scangle_it 5.385 r_dihedral_angle_1_deg 4.8 r_scbond_it 3.273 r_mcangle_it 2.211 r_mcbond_it 1.21 r_angle_refined_deg 1.105 r_angle_other_deg 0.752
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.309 r_dihedral_angle_3_deg 15.846 r_dihedral_angle_4_deg 13.76 r_scangle_it 5.385 r_dihedral_angle_1_deg 4.8 r_scbond_it 3.273 r_mcangle_it 2.211 r_mcbond_it 1.21 r_angle_refined_deg 1.105 r_angle_other_deg 0.752 r_symmetry_vdw_other 0.235 r_symmetry_hbond_refined 0.101 r_xyhbond_nbd_refined 0.095 r_symmetry_vdw_refined 0.092 r_chiral_restr 0.06 r_nbd_other 0.048 r_nbd_refined 0.031 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 806 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing