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Structure of the epsilon_1 / zeta_1 antitoxin / toxin system from Neisseria gonorrhoeae.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 294 100 mM sodium citrate pH 4.5, 1.8 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 3.54 65.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.76 α = 90 b = 149.58 β = 94.82 c = 125.09 γ = 90
Symmetry Space Group P 1 21 1
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 DECTRIS PILATUS 6M 2013-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9797 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.4 50 99.7 0.998 11.8 13.9 108038
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.8 99.6 0.152 0.826 2.5 13.7
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 2.4 48.91 108038 5687 99.73 0.22799 0.2258 0.2332 0.26956 0.2731 RANDOM 50.707
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] -0.1 0.81 -2.69 2.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.527 r_dihedral_angle_4_deg 14.877 r_dihedral_angle_3_deg 14.574 r_long_range_B_refined 7.668 r_long_range_B_other 7.66 r_scangle_other 5.88 r_dihedral_angle_1_deg 5.625 r_mcangle_other 4.557 r_mcangle_it 4.556 r_scbond_it 3.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.527 r_dihedral_angle_4_deg 14.877 r_dihedral_angle_3_deg 14.574 r_long_range_B_refined 7.668 r_long_range_B_other 7.66 r_scangle_other 5.88 r_dihedral_angle_1_deg 5.625 r_mcangle_other 4.557 r_mcangle_it 4.556 r_scbond_it 3.61 r_scbond_other 3.595 r_mcbond_it 2.941 r_mcbond_other 2.935 r_angle_refined_deg 1.383 r_angle_other_deg 0.921 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 14071 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling SHELXCD phasing Coot model building