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Arbitrium controls lysis-lysogeny through the activation of a small antirepressor protein in the majority of arbitrium-coding phages
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 16% PEG 4000, 10% 2-propanol, 100mM Hepes pH 7.5, 200mM ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.09 41.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.873 α = 90 b = 85.778 β = 96.963 c = 84.164 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 80 PIXEL DECTRIS PILATUS 6M 2023-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979257 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 1.89 42.889 99.8 0.048 0.019 0.999 21.4 7 42489
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.893 1.926 0.307 0.86 2.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.893 42.889 42487 2077 99.793 0.196 0.1938 0.1939 0.2288 0.2288 44.861
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] 0.787 2.241 -1.806 0.458
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.74 r_dihedral_angle_3_deg 13.521 r_dihedral_angle_2_deg 8.394 r_lrange_it 8.181 r_lrange_other 8.181 r_scangle_it 6.86 r_scangle_other 6.43 r_dihedral_angle_1_deg 6.284 r_scbond_it 4.881 r_scbond_other 4.452
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.74 r_dihedral_angle_3_deg 13.521 r_dihedral_angle_2_deg 8.394 r_lrange_it 8.181 r_lrange_other 8.181 r_scangle_it 6.86 r_scangle_other 6.43 r_dihedral_angle_1_deg 6.284 r_scbond_it 4.881 r_scbond_other 4.452 r_mcangle_it 4.223 r_mcangle_other 4.222 r_mcbond_it 3.315 r_mcbond_other 3.314 r_angle_refined_deg 1.953 r_angle_other_deg 0.775 r_nbd_refined 0.21 r_nbtor_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.156 r_symmetry_nbd_other 0.15 r_ncsr_local_group_3 0.149 r_ncsr_local_group_1 0.147 r_xyhbond_nbd_refined 0.146 r_ncsr_local_group_4 0.143 r_ncsr_local_group_6 0.141 r_symmetry_nbd_refined 0.134 r_ncsr_local_group_5 0.12 r_nbd_other 0.107 r_chiral_restr 0.106 r_ncsr_local_group_2 0.105 r_symmetry_nbtor_other 0.071 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3651 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing