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Structure and activity of AbiQ, a lactococcal anti-phage endoribonuclease belonging to the type-III toxin-antitoxin system
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XDD PDB ENTRY 2XDD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 buffer: 1 M potassium/sodium tartrate, 0.1 M MES, pH 6.0, drop: 200 nL 4.6 mg/mL protein + 100 nL buffer, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 43.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.14 α = 90 b = 54.51 β = 90 c = 64.24 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 2011-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9791 SOLEIL PROXIMA 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 2.16 45 99.7 0.09 17.1 13.7 9880 9880 35.49
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 2.16 2.22 99.6 0.6 3.7 13.1 753
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2XDD 2.16 27.67 9880 9880 694 0.1958 0.1958 0.1937 0.2232 0.2179 RANDOM 38.47
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] 6.209 5.4018 -11.6108
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 23.96 t_omega_torsion 3.77 t_angle_deg 1.18 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes 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 1353 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 18
Software Software Software Name Purpose DNA data collection MOLREP phasing BUSTER refinement XDS data reduction XSCALE data scaling