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Crystal structure of the multidrug binding transcriptional regulator LmrR in drug free state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ESH 2ESH, 1YYV, 1XMA experimental model PDB 1YYV 2ESH, 1YYV, 1XMA experimental model PDB 1XMA 2ESH, 1YYV, 1XMA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 30% PEG 1500, 0.1M propionic acid, cacodylate, Bis-Tris propane (PCB buffer), pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2 38.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.669 α = 90 b = 52.695 β = 90 c = 174.998 γ = 90
Symmetry Space Group C 2 2 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 2007-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.97 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 87.499 99.7 0.145 0.145 4.414 7.7 14971 14971 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 2.11 99.3 0.503 0.503 1.4 7.8 2148
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2ESH, 1YYV, 1XMA 2 87.37 2 14971 14961 756 99.44 0.221 0.221 0.219 0.272 0.2716 RANDOM 15.38
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] -1.39 0.6 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.144 r_dihedral_angle_4_deg 9.495 r_dihedral_angle_3_deg 8.327 r_scangle_it 2.765 r_scbond_it 1.793 r_dihedral_angle_1_deg 1.627 r_angle_refined_deg 1.433 r_mcangle_it 1.125 r_mcbond_it 0.719 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.144 r_dihedral_angle_4_deg 9.495 r_dihedral_angle_3_deg 8.327 r_scangle_it 2.765 r_scbond_it 1.793 r_dihedral_angle_1_deg 1.627 r_angle_refined_deg 1.433 r_mcangle_it 1.125 r_mcbond_it 0.719 r_nbtor_refined 0.306 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.212 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.123 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1692 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection