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The structure of the type III effector AvrB complexed with ADP
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 9 277 Protein (8-10 mg/ml) was mixed with well solution (100 mM Glycine, pH 9.0, 20-30% PEG 550 MME)at a 1:1 ratio. Microseeding was employed to obtain better crystals. Nucleotides were incorporated by exchanging drop and resevoir solutions with 20 l 27% PEG 500 MME and 100 mM Tris 7.5 plus 5 mM MgCl2, followed by a final exchange of this solution plus 5 mM nucleotide. Nucleotides were soaked for ~ 1 day. , VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.85 68.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.717 α = 90 b = 122.717 β = 90 c = 64.091 γ = 120
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 mirrors 2005-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
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 2.15 20 80.4 0.093 28 4.9 29955 24091 1 1 45.1
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) 2.15 2.23 32 0.318 2.63 3.3 943
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 (All) 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 2.4 20 1.5 21650 20678 999 95.2 0.233 0.232 0.232 0.2311 0.254 0.2545 RANDOM 52.8
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] 7.69 6.67 7.69 -15.38
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.5 c_scangle_it 2.05 c_mcangle_it 1.89 c_angle_deg 1.3 c_scbond_it 1.27 c_mcbond_it 1.04 c_improper_angle_d 0.81 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2389 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 35
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing