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Crystal structure of Aeromonas exotoxin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IKQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 289 12 % v/v polyethylene glycol 6000, 0.1 M MES pH 5.5, 0.1 M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.55 51.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.371 α = 90 b = 140.215 β = 101.793 c = 96.821 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 2019-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 56.36 99 0.128 0.14 0.055 0.998 12.5 12.6 60033 32.3
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 2.36 87.2 0.845 0.946 0.414 0.895 2.8 9.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1IKQ 2.3 49.575 59929 2999 98.86 0.206 0.2042 0.2082 0.2471 0.2493 37.252
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] 1.517 -2.045 -2.02 1.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.477 r_dihedral_angle_4_deg 16.035 r_dihedral_angle_3_deg 12.699 r_lrange_it 6.618 r_lrange_other 6.616 r_dihedral_angle_1_deg 6.467 r_scangle_it 4.32 r_scangle_other 4.32 r_mcangle_it 3.882 r_mcangle_other 3.882
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.477 r_dihedral_angle_4_deg 16.035 r_dihedral_angle_3_deg 12.699 r_lrange_it 6.618 r_lrange_other 6.616 r_dihedral_angle_1_deg 6.467 r_scangle_it 4.32 r_scangle_other 4.32 r_mcangle_it 3.882 r_mcangle_other 3.882 r_scbond_it 2.608 r_scbond_other 2.607 r_mcbond_it 2.329 r_mcbond_other 2.329 r_angle_refined_deg 1.331 r_angle_other_deg 1.18 r_metal_ion_refined 0.376 r_nbd_refined 0.197 r_symmetry_nbd_other 0.178 r_nbd_other 0.172 r_xyhbond_nbd_refined 0.15 r_nbtor_refined 0.149 r_symmetry_xyhbond_nbd_refined 0.144 r_symmetry_nbd_refined 0.142 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.053 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9193 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing