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Crystal structure of the flagellar cap protein FliD D2-D3 domains from Salmonella Typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H5V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 16% PEG 1000, 0.1 M sodium acetate pH 3.5, 0.2 M zinc acetate
Crystal Properties Matthews coefficient Solvent content 2.75 55.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.688 α = 90 b = 106.062 β = 90 c = 141.704 γ = 90
Symmetry Space Group P 21 21 21
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 270 2016-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 1.00004 PAL/PLS 7A (6B, 6C1)
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 2.5 30 97.4 0.084 20.2 3 40695
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 2.5 2.54
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5H5V 2.5 30 38651 2006 97.43 0.23144 0.22897 0.27847 0.2534 RANDOM 40.6
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] 0.28 -0.26 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.075 r_dihedral_angle_4_deg 19.639 r_dihedral_angle_3_deg 15.448 r_dihedral_angle_1_deg 6.013 r_angle_other_deg 4.557 r_scangle_it 1.598 r_angle_refined_deg 1.115 r_scbond_it 0.879 r_mcangle_it 0.41 r_mcbond_it 0.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.075 r_dihedral_angle_4_deg 19.639 r_dihedral_angle_3_deg 15.448 r_dihedral_angle_1_deg 6.013 r_angle_other_deg 4.557 r_scangle_it 1.598 r_angle_refined_deg 1.115 r_scbond_it 0.879 r_mcangle_it 0.41 r_mcbond_it 0.204 r_chiral_restr 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_gen_planes_other 0.003 r_bond_other_d 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_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 7091 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing