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Crystal structure of DcrB from Salmonella enterica at pH 5.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293.15 0.1 M sodium acetate pH 5.0, 34% (v/v) polyethylene glycol 5,000
Crystal Properties Matthews coefficient Solvent content 1.89 35.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.204 α = 90 b = 37.836 β = 110.128 c = 67.276 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 EIGER X 9M 2025-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.136 37.84 99.74 0.118 0.996 6.97 6.6 14748
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.136 2.17 93.35 0.491 0.849 1.9
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 (All) 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 2.136 34.671 14738 757 99.642 0.19 0.1876 0.1875 0.2384 0.2385 RANDOM 44.506
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] -1.952 0.321 0.277 1.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.663 r_dihedral_angle_6_deg 12.949 r_lrange_it 8.739 r_dihedral_angle_2_deg 8.404 r_dihedral_angle_1_deg 6.785 r_scangle_it 6.381 r_mcangle_it 4.221 r_scbond_it 4.114 r_mcbond_it 2.692 r_angle_refined_deg 1.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.663 r_dihedral_angle_6_deg 12.949 r_lrange_it 8.739 r_dihedral_angle_2_deg 8.404 r_dihedral_angle_1_deg 6.785 r_scangle_it 6.381 r_mcangle_it 4.221 r_scbond_it 4.114 r_mcbond_it 2.692 r_angle_refined_deg 1.912 r_nbtor_refined 0.274 r_symmetry_nbd_refined 0.193 r_nbd_refined 0.181 r_ncsr_local_group_1 0.151 r_chiral_restr 0.135 r_xyhbond_nbd_refined 0.131 r_symmetry_xyhbond_nbd_refined 0.111 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2270 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing