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Crystal structure of the Escherichia coli toxin-antitoxin system HipBST (HipT S57A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PU4 Emsemble model from 4PU4, 2WIU, 3TPT, 4PU3 and 4PU5 experimental model PDB 2WIU Emsemble model from 4PU4, 2WIU, 3TPT, 4PU3 and 4PU5 experimental model PDB 3TPT Emsemble model from 4PU4, 2WIU, 3TPT, 4PU3 and 4PU5 experimental model PDB 4PU3 Emsemble model from 4PU4, 2WIU, 3TPT, 4PU3 and 4PU5 experimental model PDB 4PU5 Emsemble model from 4PU4, 2WIU, 3TPT, 4PU3 and 4PU5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293.15 0.1M BICINE, 8% MPD
Crystal Properties Matthews coefficient Solvent content 3.71 66.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 281.68 α = 90 b = 106.07 β = 90.648 c = 57.56 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 16M 2018-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97625 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 49.751 99.9 0.258 0.271 0.996 10.29 9.466 66119 68.91
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 99.3 1.984 2.288 0.359 0.67 3.935
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 Emsemble model from 4PU4, 2WIU, 3TPT, 4PU3 and 4PU5 2.4 49.75 66119 3364 99.9 0.2013 0.1994 0.2106 0.2365 0.2464 RANDOM 88.87
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] -11.9926 -4.2848 6.6085 5.3841
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.64 t_omega_torsion 2.74 t_angle_deg 0.97 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8150 Nucleic Acid Atoms Solvent Atoms 474 Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction