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Crystal structure of the D100R multidrug binding transcriptional regulator LmrR in complex with Rhodium Bis-diphosphine Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DO0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 296 0.15 M Ammonium fluoride; 18% PEG 3350;
Crystal Properties Matthews coefficient Solvent content 2.3 46.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.855 α = 90 b = 35.619 β = 95.92 c = 71.651 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 PILATUS 6M 2020-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.95369 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.5 35.63 98.3 0.04 0.045 0.021 0.999 16.3 4.7 8942
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.63 98.7 0.821 0.927 0.74 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6DO0 2.5 35.63 1.35 8935 464 97.86 0.213 0.2094 0.2227 0.2801 0.2899
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 23.049 f_angle_d 1.252 f_chiral_restr 0.056 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1752 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing