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Structure of large terminase from the thermophilic bacteriophage D6E in complex with ADP (Crystal form 3)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.2 M Ammonium Sulfate, 0.1 M HEPES pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.78 55.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.878 α = 91.13 b = 102.859 β = 117.16 c = 103.029 γ = 119.17
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 2016-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 3.1 45.8 96.4 0.164 0.232 0.164 0.972 4 1.8 53693
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 3.1 3.19 94 0.832 1.177 0.832 0.336 1.7
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 MOLECULAR REPLACEMENT THROUGHOUT 3.1 45.8 50925 2705 96.6 0.2393 0.2373 0.2411 0.2779 0.2835 RANDOM 73.136
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] -2.58 -1.44 0.73 -4.02 0.6 4.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.339 r_dihedral_angle_3_deg 14.204 r_dihedral_angle_4_deg 12.348 r_dihedral_angle_1_deg 6.363 r_angle_refined_deg 1.174 r_angle_other_deg 0.886 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.339 r_dihedral_angle_3_deg 14.204 r_dihedral_angle_4_deg 12.348 r_dihedral_angle_1_deg 6.363 r_angle_refined_deg 1.174 r_angle_other_deg 0.886 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19404 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing