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Crystal structure of the large terminase nuclease from thermophilic phage G20c with bound Magnesium
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Ammonium Tartrate, 0.1 M Bis-tris pH 5.5-6.5, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.97 37.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.807 α = 90 b = 54.057 β = 91.94 c = 69.95 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-F 2016-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9796 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.2 43.78 97 0.073 0.091 0.054 0.996 7.4 2.5 98722
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 97.6 0.765 0.522 2.5
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 1.2 43.78 93879 4820 96.76 0.1845 0.1832 0.1896 0.2087 0.2094 RANDOM 14.409
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] -0.11 -0.11 0.51 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.565 r_dihedral_angle_4_deg 13.574 r_dihedral_angle_3_deg 11.169 r_dihedral_angle_1_deg 5.78 r_mcangle_it 1.322 r_angle_refined_deg 1.285 r_angle_other_deg 0.88 r_mcbond_it 0.796 r_mcbond_other 0.785 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.565 r_dihedral_angle_4_deg 13.574 r_dihedral_angle_3_deg 11.169 r_dihedral_angle_1_deg 5.78 r_mcangle_it 1.322 r_angle_refined_deg 1.285 r_angle_other_deg 0.88 r_mcbond_it 0.796 r_mcbond_other 0.785 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2928 Nucleic Acid Atoms Solvent Atoms 470 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing