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Crystal structure of LmrR with a covalent secondary amine bound 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 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 2.96 58.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.21 α = 90 b = 71.21 β = 90 c = 60.39 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 2024-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.54178
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 2.95 43.18 99.9 0.182 0.993 11.2 8.5 3794
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.13 99.9 1.044 0.369
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 2.95 43.18 3631 154 99.58 0.21829 0.21619 0.2258 0.26593 0.2689 RANDOM 64.297
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] -1.59 -0.79 -1.59 5.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.766 r_dihedral_angle_3_deg 17.231 r_dihedral_angle_4_deg 14.633 r_long_range_B_refined 6.991 r_long_range_B_other 6.988 r_dihedral_angle_1_deg 6.035 r_scangle_other 4.832 r_mcangle_it 4.443 r_mcangle_other 4.439 r_scbond_it 2.782
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.766 r_dihedral_angle_3_deg 17.231 r_dihedral_angle_4_deg 14.633 r_long_range_B_refined 6.991 r_long_range_B_other 6.988 r_dihedral_angle_1_deg 6.035 r_scangle_other 4.832 r_mcangle_it 4.443 r_mcangle_other 4.439 r_scbond_it 2.782 r_scbond_other 2.779 r_mcbond_it 2.584 r_mcbond_other 2.578 r_angle_refined_deg 0.98 r_angle_other_deg 0.691 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 892 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing