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Crystal structure of MrtR bound to 3O-C8 homoserine lactone
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, SITTING DROP 277 imidazole, MES, diethylene glycol, triethylene glycol, tetraethylene glycol, pentaethylene glycol, 2-Methyl-2,4-pentanediol (MPD), PEG 1000, PEG 3350, N-3-oxoctanoyl-L-homoserine lactone, DMSO
Crystal Properties Matthews coefficient Solvent content 2.36 47.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.334 α = 90 b = 35.554 β = 112.512 c = 61.964 γ = 90
Symmetry Space Group C 1 2 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 PILATUS4 X 4M 2025-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.442 57.2 100 0.998 10.8 6.7 46325
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.442 1.466 100 0.402 0.6 5.8
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.442 57.2 45927 2318 99.184 0.184 0.1819 0.1913 0.2319 0.2401 30.194
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] -1.936 0.227 1.935 -0.139
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.081 r_lrange_other 16.542 r_dihedral_angle_6_deg 14.459 r_scangle_it 12.213 r_scangle_other 12.209 r_dihedral_angle_3_deg 11.627 r_mcangle_other 10.175 r_mcangle_it 10.171 r_scbond_it 8.594 r_scbond_other 8.59
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.081 r_lrange_other 16.542 r_dihedral_angle_6_deg 14.459 r_scangle_it 12.213 r_scangle_other 12.209 r_dihedral_angle_3_deg 11.627 r_mcangle_other 10.175 r_mcangle_it 10.171 r_scbond_it 8.594 r_scbond_other 8.59 r_mcbond_it 7.242 r_mcbond_other 7.236 r_dihedral_angle_2_deg 6.793 r_dihedral_angle_1_deg 5.1 r_rigid_bond_restr 3.54 r_angle_refined_deg 1.47 r_angle_other_deg 0.532 r_symmetry_nbd_refined 0.265 r_nbd_other 0.247 r_nbd_refined 0.22 r_symmetry_xyhbond_nbd_refined 0.218 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.173 r_symmetry_xyhbond_nbd_other 0.131 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.074 r_xyhbond_nbd_other 0.046 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1856 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction autoPROC data scaling PHASER phasing