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Structure of the AvrBs3-DNA complex provides new insights into the initial thymine-recognition mechanism
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V6T PDB ENTRY 3V6T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1M MES PH=6.5, 5-15% PEG3350, 5-15% 2-PROPANOL
Crystal Properties Matthews coefficient Solvent content 2.31 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.11 α = 90 b = 100.25 β = 102.55 c = 61.37 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 PIXEL DECTRIS PILATUS 6M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.55 32.29 93 0.04 11.79 2.2 25764 1.3
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 2.55 2.62 95.1 0.62 1.31 2.07
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3V6T 2.55 32.29 25764 1373 93.27 0.23857 0.23578 0.2461 0.28983 0.3024 RANDOM 72.161
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] 0.72 -0.08 -1.27 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.084 r_dihedral_angle_4_deg 22.616 r_dihedral_angle_3_deg 21.737 r_dihedral_angle_1_deg 7.588 r_angle_refined_deg 1.897 r_chiral_restr 0.112 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.084 r_dihedral_angle_4_deg 22.616 r_dihedral_angle_3_deg 21.737 r_dihedral_angle_1_deg 7.588 r_angle_refined_deg 1.897 r_chiral_restr 0.112 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4772 Nucleic Acid Atoms 875 Solvent Atoms 175 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing