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The crystal structure of phytoplasmal effector causing phyllody symptoms 1 (PHYL1)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.05 M cadmium sulfate hydrate, 0.1 M HEPES pH 7.5 and 1.0 M sodium acetate trihydrate
Crystal Properties Matthews coefficient Solvent content 2.79 55.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.006 α = 90 b = 65.006 β = 90 c = 193.432 γ = 120
Symmetry Space Group P 63 2 2
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 RAYONIX MX300-HS 2016-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
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 2.34 20 98.9 0.036 44.6 8 10840
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 2.34 2.42 98.9 1.012 2 7.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.34 20 8698 456 83.48 0.25704 0.25631 0.2573 0.27042 0.2808 RANDOM 47.451
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] 0.41 0.2 0.41 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.281 r_dihedral_angle_3_deg 16.856 r_long_range_B_refined 10.042 r_long_range_B_other 9.975 r_scangle_other 5.895 r_dihedral_angle_4_deg 4.932 r_mcangle_it 4.866 r_mcangle_other 4.863 r_dihedral_angle_1_deg 4.206 r_angle_other_deg 3.475
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.281 r_dihedral_angle_3_deg 16.856 r_long_range_B_refined 10.042 r_long_range_B_other 9.975 r_scangle_other 5.895 r_dihedral_angle_4_deg 4.932 r_mcangle_it 4.866 r_mcangle_other 4.863 r_dihedral_angle_1_deg 4.206 r_angle_other_deg 3.475 r_scbond_it 3.329 r_scbond_other 3.326 r_mcbond_it 2.885 r_mcbond_other 2.877 r_angle_refined_deg 1.252 r_chiral_restr 0.07 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 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 1188 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling Blu-Ice data collection BUCCANEER model building HKL-2000 data reduction SHELX phasing