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Crystal structure of Repeats-in-Toxin-like domain from Aeromonas hydrophila
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 295 PEG 8000, MES, Acetate calcium
Crystal Properties Matthews coefficient Solvent content 2.3 46.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.603 α = 90 b = 103.327 β = 90 c = 95.71 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS3 6M 2018-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.53484 CLSI 08ID-1
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 1.95 50 100 0.127 0.132 0.037 0.999 15.9 12.9 24829 28.365
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 100 1.657 0.675 0.73 2 12.9
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 SAD THROUGHOUT 1.95 48.75 23607 1197 99.98 0.20587 0.20322 0.2096 0.2575 0.2587 RANDOM 34.498
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] -0.75 0.88 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.914 r_dihedral_angle_3_deg 12.798 r_dihedral_angle_4_deg 10.349 r_long_range_B_refined 8.235 r_long_range_B_other 8.173 r_dihedral_angle_1_deg 7.912 r_scangle_other 5.47 r_mcangle_it 4.67 r_mcangle_other 4.668 r_scbond_it 3.719
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.914 r_dihedral_angle_3_deg 12.798 r_dihedral_angle_4_deg 10.349 r_long_range_B_refined 8.235 r_long_range_B_other 8.173 r_dihedral_angle_1_deg 7.912 r_scangle_other 5.47 r_mcangle_it 4.67 r_mcangle_other 4.668 r_scbond_it 3.719 r_scbond_other 3.717 r_mcbond_it 3.256 r_mcbond_other 3.251 r_angle_refined_deg 1.596 r_angle_other_deg 1.376 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 2100 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling AutoSol phasing