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Structure of YIUA from Yersinia ruckeri
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 8.5 298 0.1 M Tris-HCl, 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.97 58.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.598 α = 90 b = 68.474 β = 96.75 c = 112.908 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 2024-07-12 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) 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 2.14 112.16 86.1 0.25 0.16 0.99 5.7 6.2 16162
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 2.14 2.57 53.1 0.84 0.64 0.57 1.8
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 2.14 112.13 15393 768 45.42 0.21233 0.2076 0.2139 0.3097 0.3087 RANDOM 22.067
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] 0.38 -0.39 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.665 r_dihedral_angle_1_deg 6.538 r_dihedral_angle_2_deg 5.531 r_long_range_B_refined 4.913 r_long_range_B_other 4.872 r_mcangle_it 2.305 r_mcangle_other 2.305 r_scangle_other 2.199 r_mcbond_it 1.321 r_mcbond_other 1.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.665 r_dihedral_angle_1_deg 6.538 r_dihedral_angle_2_deg 5.531 r_long_range_B_refined 4.913 r_long_range_B_other 4.872 r_mcangle_it 2.305 r_mcangle_other 2.305 r_scangle_other 2.199 r_mcbond_it 1.321 r_mcbond_other 1.321 r_angle_refined_deg 1.274 r_scbond_it 1.255 r_scbond_other 1.255 r_angle_other_deg 0.431 r_chiral_restr 0.056 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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 5125 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing