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Crystal structure of AgrA LytTR domain in complex with promoters
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 6% Tacsimate, 0.1M MES monohydrate pH 6.0, 25% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.66 53.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.02 α = 90 b = 145.6 β = 93.09 c = 62.1 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 CCD MAR CCD 165 mm 2014-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97625 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.05 62.01 99.3 0.096 6.9 3.8 13297
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.05 3.26 99.4 0.825 1.34 3.8
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 THROUGHOUT 3.05 62.01 12641 654 99.3 0.26347 0.26139 0.2611 0.30501 0.3066 RANDOM 113.393
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] -1.75 -10.52 -0.05 2.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.084 r_dihedral_angle_4_deg 14.735 r_long_range_B_refined 13.826 r_long_range_B_other 13.826 r_dihedral_angle_3_deg 12.701 r_scangle_other 7.837 r_mcangle_it 7.794 r_mcangle_other 7.793 r_dihedral_angle_1_deg 6.014 r_mcbond_it 4.783
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.084 r_dihedral_angle_4_deg 14.735 r_long_range_B_refined 13.826 r_long_range_B_other 13.826 r_dihedral_angle_3_deg 12.701 r_scangle_other 7.837 r_mcangle_it 7.794 r_mcangle_other 7.793 r_dihedral_angle_1_deg 6.014 r_mcbond_it 4.783 r_mcbond_other 4.782 r_scbond_it 4.745 r_scbond_other 4.744 r_angle_other_deg 1.813 r_angle_refined_deg 1.242 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_bond_other_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.007 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 3186 Nucleic Acid Atoms 1300 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALA data reduction SCALA data scaling PHENIX phasing