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crystal structure of effect protein AvrptoB complexed with kinase Pto
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HGL PDB ENTRIES 3HGL for AvrPtoB AND 2QKW for Pto experimental model PDB 2QKW PDB ENTRIES 3HGL for AvrPtoB AND 2QKW for Pto
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 293 0.1M tri-Sodium Citrate dihydrate, 17.5% (w/v) Polyethylene Glycol 3350, 0.1mM Tris-HCl pH 7.9, 10.0mM phenol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.55 51.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.07 α = 90 b = 104.47 β = 90 c = 298.86 γ = 90
Symmetry Space Group P 21 21 21
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 2008-01-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 3.3 99 99.8 0.081 22.3 5.6 29886 2 2.9
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) 3.3 3.37 99.6 0.53 2.9 5.3
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 ENTRIES 3HGL for AvrPtoB AND 2QKW for Pto 3.3 20 28059 1506 99.65 0.31775 0.31706 0.3292 0.3305 0.3421 RANDOM 81.806
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] -5.99 14.94 -8.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.746 r_dihedral_angle_3_deg 17.929 r_dihedral_angle_4_deg 16.832 r_dihedral_angle_1_deg 4.641 r_mcangle_it 3.856 r_mcbond_it 2.485 r_scangle_it 2.401 r_scbond_it 1.725 r_angle_refined_deg 1.32 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.746 r_dihedral_angle_3_deg 17.929 r_dihedral_angle_4_deg 16.832 r_dihedral_angle_1_deg 4.641 r_mcangle_it 3.856 r_mcbond_it 2.485 r_scangle_it 2.401 r_scbond_it 1.725 r_angle_refined_deg 1.32 r_nbtor_refined 0.312 r_nbd_refined 0.272 r_symmetry_vdw_refined 0.27 r_xyhbond_nbd_refined 0.191 r_chiral_restr 0.089 r_symmetry_hbond_refined 0.06 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11599 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection SOLVE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing