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Crystal structure of the large terminase nuclease from thermophilic phage G20c
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.2 M Lithium Sulfate, 0.1 M Bis-tris pH 5.5, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.34 47.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.102 α = 90 b = 55.102 β = 90 c = 95.759 γ = 120
Symmetry Space Group P 32 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 PILATUS 6M-F 2016-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 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 2.15 47.72 95.6 0.043 0.055 0.035 0.999 10.3 2.2 9183
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.21 90.6 0.804 1.043 0.658 0.365 2.2 721
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 2.15 47.72 8735 433 94.96 0.2044 0.2004 0.2059 0.2811 0.2884 RANDOM 54.596
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] 0.27 0.14 0.27 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.342 r_dihedral_angle_3_deg 12.077 r_dihedral_angle_4_deg 11.384 r_dihedral_angle_1_deg 6.177 r_mcangle_it 4.68 r_mcbond_it 3.1 r_mcbond_other 3.1 r_angle_refined_deg 1.291 r_angle_other_deg 0.861 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.342 r_dihedral_angle_3_deg 12.077 r_dihedral_angle_4_deg 11.384 r_dihedral_angle_1_deg 6.177 r_mcangle_it 4.68 r_mcbond_it 3.1 r_mcbond_other 3.1 r_angle_refined_deg 1.291 r_angle_other_deg 0.861 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1407 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing