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Crystal structure of the large terminase nuclease from thermophilic phage G20c with bound Cobalt
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 1.92 36.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.937 α = 90 b = 53.895 β = 91.62 c = 69.751 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 1.6 42.92 95.7 0.072 0.092 0.057 0.997 6.6 2.1 40243
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 1.6 1.63 89.5 0.725 0.604 2
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 1.6 42.92 38195 2038 95.44 0.1868 0.1849 0.1935 0.224 0.2315 RANDOM 22.409
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] 1.99 -0.82 -1.03 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.908 r_dihedral_angle_4_deg 14.573 r_dihedral_angle_3_deg 12.037 r_dihedral_angle_1_deg 5.794 r_mcangle_it 1.818 r_angle_refined_deg 1.273 r_mcbond_it 1.083 r_mcbond_other 1.081 r_angle_other_deg 0.883 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.908 r_dihedral_angle_4_deg 14.573 r_dihedral_angle_3_deg 12.037 r_dihedral_angle_1_deg 5.794 r_mcangle_it 1.818 r_angle_refined_deg 1.273 r_mcbond_it 1.083 r_mcbond_other 1.081 r_angle_other_deg 0.883 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2914 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 2
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing