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Structure of YIUA from Yersinia ruckeri with Iron and DHB-L-Arg-L-Ser
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B2X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.2 M Lithium Sulfate; 0.1 M HEPES pH 7.5; 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.34 47.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.073 α = 90 b = 80.018 β = 89.86 c = 223.696 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 120 PIXEL DECTRIS EIGER2 XE 16M 2024-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97627 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.45 75.56 99.5 0.13 1 7.9 7.2 103842 23
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 2.45 2.49 0.37 0.23 0.97 2.9
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 MOLECULAR REPLACEMENT THROUGHOUT 2.45 75.56 98619 5183 99.43 0.24845 0.24694 0.2519 0.27667 0.2841 RANDOM 34.925
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] -6.79 -0.01 10.71 -3.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.738 r_dihedral_angle_2_deg 7.691 r_long_range_B_refined 7.308 r_long_range_B_other 7.308 r_dihedral_angle_1_deg 5.858 r_scangle_other 5.153 r_mcangle_other 5.145 r_mcangle_it 5.144 r_mcbond_it 3.297 r_mcbond_other 3.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.738 r_dihedral_angle_2_deg 7.691 r_long_range_B_refined 7.308 r_long_range_B_other 7.308 r_dihedral_angle_1_deg 5.858 r_scangle_other 5.153 r_mcangle_other 5.145 r_mcangle_it 5.144 r_mcbond_it 3.297 r_mcbond_other 3.296 r_scbond_it 3.257 r_scbond_other 3.223 r_angle_refined_deg 1.492 r_angle_other_deg 0.531 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 20889 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 546
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing