☰ Navigation Tabs
Crystal structure of AgrA LytTR domain in complex with promoters
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 0.1M Sodium citrate tribasic dihydrate pH 5.6, 20% 2-propanol, 20% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.24 45.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.17 α = 91.09 b = 61.32 β = 97.48 c = 64.1 γ = 94.02
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 2013-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95373 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 2.26 44.69 97.1 0.1 12.6 3.9 29349
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 2.3 2.38 96.3 0.56 2.7 3.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 2.3 44.69 27875 1465 97.1 0.21303 0.21127 0.2475 0.2765 RANDOM 44.054
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] -2.04 -1.73 -0.65 1.04 0.67 1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.834 r_dihedral_angle_4_deg 16.597 r_dihedral_angle_3_deg 14.551 r_long_range_B_refined 10.521 r_long_range_B_other 10.521 r_dihedral_angle_1_deg 6.93 r_scangle_other 5.725 r_mcangle_it 4.388 r_mcangle_other 4.387 r_scbond_it 3.567
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.834 r_dihedral_angle_4_deg 16.597 r_dihedral_angle_3_deg 14.551 r_long_range_B_refined 10.521 r_long_range_B_other 10.521 r_dihedral_angle_1_deg 6.93 r_scangle_other 5.725 r_mcangle_it 4.388 r_mcangle_other 4.387 r_scbond_it 3.567 r_scbond_other 3.566 r_mcbond_it 2.857 r_mcbond_other 2.854 r_angle_other_deg 1.761 r_angle_refined_deg 1.461 r_chiral_restr 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 3223 Nucleic Acid Atoms 1983 Solvent Atoms 93 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement SCALA data reduction SCALA data scaling PHASER phasing