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Crystal structure of AgrA LytTR domain in complex with promoters
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BS1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 0.05M Calcium chloride dihydrate
0.1M MES monohydrate pH 6.0
45% PEG 200
Crystal Properties Matthews coefficient Solvent content 2.44 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.03 α = 90 b = 92.87 β = 98.59 c = 45.15 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 2013-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95372 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 1.9 35.02 100 0.065 12.6 4.4 29281
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 1.9 2 100 0.662 2.1 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 3BS1 1.9 35.02 27856 1422 99.97 0.18931 0.18757 0.22475 0.2286 RANDOM 39.663
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] 1.68 1.48 -0.58 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.158 r_dihedral_angle_4_deg 19.466 r_dihedral_angle_3_deg 13.335 r_long_range_B_refined 8.661 r_long_range_B_other 8.66 r_dihedral_angle_1_deg 6.999 r_scangle_other 5.11 r_mcangle_it 3.456 r_mcangle_other 3.455 r_scbond_it 3.275
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.158 r_dihedral_angle_4_deg 19.466 r_dihedral_angle_3_deg 13.335 r_long_range_B_refined 8.661 r_long_range_B_other 8.66 r_dihedral_angle_1_deg 6.999 r_scangle_other 5.11 r_mcangle_it 3.456 r_mcangle_other 3.455 r_scbond_it 3.275 r_scbond_other 3.268 r_mcbond_it 2.316 r_mcbond_other 2.302 r_angle_other_deg 1.396 r_angle_refined_deg 1.365 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.004 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 1645 Nucleic Acid Atoms 999 Solvent Atoms 166 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement SCALA data reduction SCALA data scaling PHASER phasing