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Structure of a toxin-antitoxin system bound to its substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GVN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 293 0.2 M sodium acetate, 16% (w/v) PEG1500 and 7% (v/v) MPD, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.7 54.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.8 α = 90 b = 79.99 β = 90 c = 195.17 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 PIXEL PSI PILATUS 6M 2010-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1 SLS X10SA
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 2.7 50 95.9 0.048 26.5 7.3 26528 25432
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 2.7 2.8 86.4 0.548 4.1 7.1
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 FOURIER SYNTHESIS THROUGHOUT 1GVN 2.7 46.52 26528 25131 1323 100 0.21237 0.20968 0.2063 0.26309 0.2559 RANDOM 76.864
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] -2.24 0.54 1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.178 r_dihedral_angle_3_deg 16.172 r_dihedral_angle_4_deg 14.828 r_dihedral_angle_1_deg 4.838 r_scangle_it 1.59 r_angle_refined_deg 1.106 r_scbond_it 0.947 r_mcangle_it 0.662 r_mcbond_it 0.388 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.178 r_dihedral_angle_3_deg 16.172 r_dihedral_angle_4_deg 14.828 r_dihedral_angle_1_deg 4.838 r_scangle_it 1.59 r_angle_refined_deg 1.106 r_scbond_it 0.947 r_mcangle_it 0.662 r_mcbond_it 0.388 r_nbtor_refined 0.3 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.197 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 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_refined 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5767 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement CNS refinement XDS data scaling XDS data reduction CNS phasing