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Crystal structure of the flagellar cap protein FliD D2-D3 domains from Serratia marcescens in Space group I422
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XLJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 291 2.5 M sodium chloride, 0.1 M imidazole, pH 8.0, and 0.2 M zinc acetate
Crystal Properties Matthews coefficient Solvent content 3.51 64.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.362 α = 90 b = 121.362 β = 90 c = 249.266 γ = 90
Symmetry Space Group I 4 2 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 CCD ADSC QUANTUM 270 2016-12-18 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 3.05 30 96.9 0.125 25.9 6.9 17805
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 3.05 3.1 0.476
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 5XLJ 3.05 30 16662 841 96.34 0.24069 0.23841 0.2377 0.28654 0.286 RANDOM 47.564
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 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.194 r_dihedral_angle_3_deg 16.767 r_dihedral_angle_4_deg 13.061 r_dihedral_angle_1_deg 6.26 r_scangle_it 2.686 r_scbond_it 1.517 r_angle_refined_deg 1.401 r_angle_other_deg 0.904 r_mcangle_it 0.743 r_mcbond_it 0.358
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.194 r_dihedral_angle_3_deg 16.767 r_dihedral_angle_4_deg 13.061 r_dihedral_angle_1_deg 6.26 r_scangle_it 2.686 r_scbond_it 1.517 r_angle_refined_deg 1.401 r_angle_other_deg 0.904 r_mcangle_it 0.743 r_mcbond_it 0.358 r_mcbond_other 0.073 r_chiral_restr 0.068 r_bond_refined_d 0.015 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_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 3998 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing