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Crystal structure of engineered LmrR mutant with a covalent secondary amine cofactor link to Cystein on position 57
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I8N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293.15 0.1 M di-Ammonium phosphate, 0.1 M Tris-HCl, pH 8.5, 0.5 M di-Sodium phosphate and
0.5 M di-Potassium phosphate
Crystal Properties Matthews coefficient Solvent content 3.04 59.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.717 α = 90 b = 71.717 β = 90 c = 60.969 γ = 120
Symmetry Space Group P 32 1 2
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 Bruker PHOTON II 2024-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.54184
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 2.7 43.55 100 0.102 0.049 0.999 17.7 9.9 5066
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 100 0.951 0.5
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 2.7 43.55 4838 212 99.88 0.22347 0.22138 0.2277 0.26425 0.2647 RANDOM 65.003
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] -0.49 -0.24 -0.49 1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.028 r_long_range_B_refined 12.687 r_long_range_B_other 12.682 r_scangle_other 10.601 r_mcangle_it 9.633 r_mcangle_other 9.631 r_dihedral_angle_2_deg 7.641 r_scbond_it 7.134 r_scbond_other 7.127 r_mcbond_it 6.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.028 r_long_range_B_refined 12.687 r_long_range_B_other 12.682 r_scangle_other 10.601 r_mcangle_it 9.633 r_mcangle_other 9.631 r_dihedral_angle_2_deg 7.641 r_scbond_it 7.134 r_scbond_other 7.127 r_mcbond_it 6.474 r_mcbond_other 6.446 r_dihedral_angle_1_deg 5.178 r_angle_refined_deg 1.536 r_angle_other_deg 0.534 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 904 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing