☰ Navigation Tabs
Engineered LmrR with V15 replaced by unnatural amino acid 4-amino-L-phenyl-cysteine
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 PEGRX2 containing 1.8M Ammonium sulfate, 0.1M Bis-Tris, pH 6.5 and 2% (v/v) PEG 550
Crystal Properties Matthews coefficient Solvent content 2.92 57.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.62 α = 90 b = 70.62 β = 90 c = 61.33 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 multilayer 2024-01-12 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) 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 43.34 100 0.099 0.035 0.999 17.7 8.9 4944
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 1.094 0.411
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 43.34 4719 208 99.88 0.2439 0.24175 0.2485 0.28605 0.2945 RANDOM 66.893
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] -1.26 -0.63 -1.26 4.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.543 r_dihedral_angle_3_deg 17.148 r_dihedral_angle_4_deg 13.085 r_long_range_B_refined 5.971 r_long_range_B_other 5.968 r_dihedral_angle_1_deg 4.843 r_mcangle_other 4.471 r_mcangle_it 4.469 r_scangle_other 3.598 r_mcbond_it 2.636
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.543 r_dihedral_angle_3_deg 17.148 r_dihedral_angle_4_deg 13.085 r_long_range_B_refined 5.971 r_long_range_B_other 5.968 r_dihedral_angle_1_deg 4.843 r_mcangle_other 4.471 r_mcangle_it 4.469 r_scangle_other 3.598 r_mcbond_it 2.636 r_mcbond_other 2.587 r_scbond_it 2.036 r_scbond_other 2.031 r_angle_refined_deg 0.937 r_angle_other_deg 0.712 r_chiral_restr 0.055 r_bond_refined_d 0.005 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 909 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing