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Crystal structure of multidrug binding transcriptional regulator LmrR complexed with Daunomycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F8B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 25% PEG1500, 0.1M malonic acid/imidazol/boric (MIB) buffer, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.34 47.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.45 α = 90 b = 53.025 β = 90 c = 147.116 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 mirrors 2006-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.92 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 49.884 99.4 0.071 6.6 3.4 14655 14655 2
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 2.2 2.32 99.9 0.273 0.273 2.7 3.5 2074
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3F8B 2.2 49.88 14615 13853 762 100 0.23465 0.23205 0.2277 0.2796 0.278 RANDOM 24.347
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] -1.78 3.32 -1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.087 r_dihedral_angle_3_deg 18.916 r_dihedral_angle_4_deg 13.174 r_dihedral_angle_1_deg 5.729 r_scangle_it 2.798 r_scbond_it 1.687 r_mcangle_it 1.131 r_mcbond_it 0.684 r_angle_refined_deg 0.651 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.087 r_dihedral_angle_3_deg 18.916 r_dihedral_angle_4_deg 13.174 r_dihedral_angle_1_deg 5.729 r_scangle_it 2.798 r_scbond_it 1.687 r_mcangle_it 1.131 r_mcbond_it 0.684 r_angle_refined_deg 0.651 r_nbtor_refined 0.316 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.166 r_chiral_restr 0.063 r_bond_refined_d 0.016 r_gen_planes_refined 0.001 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1832 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 38
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection