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Crystal structure of DcrB from Salmonella enterica at pH 4.0
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 4 293 0.1 M sodium acetate pH 4.0, 30% (v/v) polyethylene glycol 5,000
Crystal Properties Matthews coefficient Solvent content 1.88 34.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.376 α = 90 b = 37.639 β = 110.171 c = 66.965 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 1.729 32.313 97.74 0.053 0.999 15.6 7 26846
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 1.729 1.76 0.804 0.822 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 (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 1.729 32.313 26846 1381 97.721 0.201 0.1997 0.1997 0.228 0.2277 RANDOM 42.693
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] 0.258 1.56 -2.451 0.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.923 r_dihedral_angle_3_deg 12.73 r_lrange_it 11.819 r_scangle_it 10.56 r_scbond_it 7.781 r_dihedral_angle_1_deg 6.222 r_mcangle_it 5.401 r_dihedral_angle_2_deg 4.739 r_mcbond_it 4.339 r_angle_refined_deg 1.661
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.923 r_dihedral_angle_3_deg 12.73 r_lrange_it 11.819 r_scangle_it 10.56 r_scbond_it 7.781 r_dihedral_angle_1_deg 6.222 r_mcangle_it 5.401 r_dihedral_angle_2_deg 4.739 r_mcbond_it 4.339 r_angle_refined_deg 1.661 r_nbtor_refined 0.271 r_nbd_refined 0.166 r_ncsr_local_group_1 0.154 r_symmetry_nbd_refined 0.138 r_chiral_restr 0.121 r_symmetry_xyhbond_nbd_refined 0.105 r_xyhbond_nbd_refined 0.094 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2274 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing