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Toxin fold for microbial attack and plant defense
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GNU PDB ENTRY 3GNU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 0.1M Tris HCl pH 9.0, 20% PEG 4000, 0.5M MgCl2, 5% methanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.61 52.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.63 α = 90 b = 140.9 β = 90 c = 49.62 γ = 90
Symmetry Space Group C 2 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 MARMOSAIC 225 mm CCD 2004-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0052 ESRF ID23-1
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 1.35 25 98.3 0.05 3.8 53077 53077 -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) 1.35 1.45 92.1 0.281 4.2 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3GNU 1.35 23.4 53077 50423 2654 100 0.15694 0.15554 0.1542 0.18363 0.1819 RANDOM 13.508
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] 0.25 -0.2 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.5 r_dihedral_angle_4_deg 15.874 r_dihedral_angle_3_deg 11.889 r_dihedral_angle_1_deg 5.809 r_sphericity_free 3.461 r_scangle_it 2.569 r_sphericity_bonded 2.472 r_scbond_it 1.797 r_mcangle_it 1.412 r_angle_refined_deg 1.218
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.5 r_dihedral_angle_4_deg 15.874 r_dihedral_angle_3_deg 11.889 r_dihedral_angle_1_deg 5.809 r_sphericity_free 3.461 r_scangle_it 2.569 r_sphericity_bonded 2.472 r_scbond_it 1.797 r_mcangle_it 1.412 r_angle_refined_deg 1.218 r_rigid_bond_restr 0.957 r_mcbond_it 0.869 r_nbtor_refined 0.306 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.156 r_xyhbond_nbd_refined 0.152 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.078 r_metal_ion_refined 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1799 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 2
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction