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Structure of the tail fibre from an extracellular contractile injection system from Photorhabdus bacteria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Created with AlphaFold colab
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 290 0.02 M CaCl2 dihydrate, 0.1M Na acetate pH 4.6, 30% MPD
Crystal Properties Matthews coefficient Solvent content 2.8 56.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.458 α = 90 b = 53.536 β = 95.65 c = 220.66 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER2 XE 16M 2022-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97951 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.3 60.03 100 0.103 0.113 0.046 0.997 9.7 6.2 70537 37.715
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.35 99.5 0.669 0.735 0.301 0.941 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.3 60.03 66849 3581 99.94 0.18191 0.17902 0.186 0.23582 0.2379 RANDOM 42.635
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] -3.71 -3.47 2.05 2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.831 r_dihedral_angle_2_deg 9.362 r_dihedral_angle_1_deg 8.908 r_long_range_B_refined 8.758 r_long_range_B_other 8.757 r_scangle_other 6.858 r_mcangle_it 5.971 r_mcangle_other 5.97 r_scbond_it 4.508 r_scbond_other 4.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.831 r_dihedral_angle_2_deg 9.362 r_dihedral_angle_1_deg 8.908 r_long_range_B_refined 8.758 r_long_range_B_other 8.757 r_scangle_other 6.858 r_mcangle_it 5.971 r_mcangle_other 5.97 r_scbond_it 4.508 r_scbond_other 4.507 r_mcbond_it 4.145 r_mcbond_other 4.144 r_angle_refined_deg 1.482 r_angle_other_deg 0.485 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 9109 Nucleic Acid Atoms Solvent Atoms 517 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing xia2 data reduction