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The structure of the type III effector AvrB complexed with a high-affinity RIN4 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NH1 PDB entry 1NH1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 1:2-3 ratio of protein to peptide with AvrB at ~12 mg/ml mixed with an equal volume of well solution (100 mM Tris, pH 7.5, 20-30% PEG 550 MME), VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.98 38.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.884 α = 90 b = 58.166 β = 89.92 c = 119.767 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE RIGAKU RAXIS IV Osmic Confocal "Blue" 2004-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.2 99 88.8 0.109 11 29016 29016 1 1 36.2
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) 2.2 2.28 72.7 0.437 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 1NH1 2.3 19.96 1.5 28265 26385 1273 93.2 0.21 0.21 0.2067 0.26 0.2542 RANDOM 32.1
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] 2.31 -0.42 0.24 -2.54
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.9 c_scangle_it 4.29 c_scbond_it 3.1 c_mcangle_it 3.05 c_mcbond_it 1.96 c_angle_deg 1.2 c_improper_angle_d 0.75 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.9 c_scangle_it 4.29 c_scbond_it 3.1 c_mcangle_it 3.05 c_mcbond_it 1.96 c_angle_deg 1.2 c_improper_angle_d 0.75 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5012 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 44
Software Software Software Name Purpose CNS refinement CrystalClear data collection HKL-3000 data reduction HKL-3000 data scaling AMoRE phasing