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Structure of AgrA LytTR domain in complex with promoters
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 0.1M Bis-Tris pH 6.0,
40% PEG 400.
Crystal Properties Matthews coefficient Solvent content 2.72 54.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.77 α = 90 b = 47.77 β = 90 c = 100.25 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 300 mm plate 2012-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002 1.54179
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 2.38 50.12 99.7 0.081 9.6 4.2 8820
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 2.4 2.49 100 0.461 2.9 4.5
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 2.4 47.77 8347 437 99.6 0.2026 0.20084 0.2076 0.23752 0.2403 RANDOM 43.988
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] 1.8 1.8 -3.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.947 r_dihedral_angle_4_deg 16.831 r_dihedral_angle_3_deg 14.175 r_long_range_B_refined 9.083 r_long_range_B_other 9.083 r_scangle_other 6.691 r_dihedral_angle_1_deg 6.327 r_mcangle_it 4.63 r_mcangle_other 4.629 r_scbond_it 4.485
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.947 r_dihedral_angle_4_deg 16.831 r_dihedral_angle_3_deg 14.175 r_long_range_B_refined 9.083 r_long_range_B_other 9.083 r_scangle_other 6.691 r_dihedral_angle_1_deg 6.327 r_mcangle_it 4.63 r_mcangle_other 4.629 r_scbond_it 4.485 r_scbond_other 4.485 r_mcbond_it 3.115 r_mcbond_other 3.092 r_angle_refined_deg 1.537 r_angle_other_deg 1.306 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.002 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 865 Nucleic Acid Atoms 650 Solvent Atoms 22 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement SCALA data reduction SCALA data scaling PHASER phasing