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The Crystal Structure of the Salmonella Type III Secretion System Tip Protein SipD in Complex with Deoxycholate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P7N PDB ENTRY 2P7N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.2 M magnesium formate dihydrate, 15% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.26 45.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.931 α = 90 b = 52.327 β = 90.34 c = 57.311 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 210r 2009-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-BM 1.0 APS 17-BM
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 1.9 27.98 98.5 0.053 20.3 3.6 46924 44447
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.95 86.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2P7N 1.9 25.33 46924 44441 2373 98.61 0.1992 0.19618 0.1952 0.25678 0.2537 RANDOM 28.76
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] -0.02 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.97 r_dihedral_angle_3_deg 14.438 r_dihedral_angle_4_deg 13.233 r_dihedral_angle_1_deg 4.873 r_scangle_it 3.578 r_scbond_it 2.562 r_mcangle_it 1.547 r_angle_refined_deg 1.387 r_mcbond_it 1.024 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.97 r_dihedral_angle_3_deg 14.438 r_dihedral_angle_4_deg 13.233 r_dihedral_angle_1_deg 4.873 r_scangle_it 3.578 r_scbond_it 2.562 r_mcangle_it 1.547 r_angle_refined_deg 1.387 r_mcbond_it 1.024 r_nbtor_refined 0.299 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_metal_ion_refined 0.009 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 4315 Nucleic Acid Atoms Solvent Atoms 485 Heterogen Atoms 29
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling