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The crystal structure of Dickeya dadantii GspB from the type 2 secretion system
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291.15 initial hit from nano drop. Scaled up using whisker streak seeding.
0.2M MgCl, 0.1M Tris, 30% w/v PEG4000, pH8.5
Crystal Properties Matthews coefficient Solvent content 2.17 43.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.21 α = 90 b = 36.21 β = 90 c = 131.28 γ = 90
Symmetry Space Group P 43 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 PIXEL PSI PILATUS 6M 2013-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 1.0 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.02 36.03 99.2 30.6 8.9 6380
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 3oss 2.05 34.91 5276 591 97.39 0.21303 0.20853 0.2195 0.25421 0.2531 RANDOM 55.749
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] -0.4 -0.4 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.088 r_dihedral_angle_3_deg 14.024 r_dihedral_angle_1_deg 8.603 r_dihedral_angle_4_deg 6.034 r_long_range_B_refined 4.68 r_long_range_B_other 4.677 r_scangle_other 2.911 r_mcangle_it 2.608 r_mcangle_other 2.605 r_scbond_it 1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.088 r_dihedral_angle_3_deg 14.024 r_dihedral_angle_1_deg 8.603 r_dihedral_angle_4_deg 6.034 r_long_range_B_refined 4.68 r_long_range_B_other 4.677 r_scangle_other 2.911 r_mcangle_it 2.608 r_mcangle_other 2.605 r_scbond_it 1.86 r_scbond_other 1.859 r_angle_refined_deg 1.682 r_mcbond_other 1.666 r_mcbond_it 1.665 r_angle_other_deg 0.95 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 661 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction xia2 data scaling PHASER phasing