☰ Navigation Tabs
Crystal structure of thymoligase, a substrate-tailored peptiligase variant
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 294 1.0 M Ammonium Sulfate, 0.1 M Bis-tris, 1% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.1 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.478 α = 90 b = 40.061 β = 106.04 c = 64.25 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 2017-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
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 2.24 45.6 91.6 0.102 0.071 0.99 7.8 3.5 10355 21.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.24 2.32 92.1 0.479 0.35 0.78
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 2.24 45.6 9833 513 91.17 0.19004 0.1877 0.1961 0.22998 0.2273 RANDOM 24.68
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] 1.79 -1.41 -2.03 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.026 r_dihedral_angle_3_deg 13.928 r_dihedral_angle_4_deg 10.75 r_dihedral_angle_1_deg 5.4 r_long_range_B_refined 3.573 r_long_range_B_other 3.478 r_scangle_other 2.214 r_mcangle_it 1.74 r_mcangle_other 1.739 r_scbond_it 1.481
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.026 r_dihedral_angle_3_deg 13.928 r_dihedral_angle_4_deg 10.75 r_dihedral_angle_1_deg 5.4 r_long_range_B_refined 3.573 r_long_range_B_other 3.478 r_scangle_other 2.214 r_mcangle_it 1.74 r_mcangle_other 1.739 r_scbond_it 1.481 r_scbond_other 1.401 r_angle_refined_deg 1.356 r_mcbond_other 1.069 r_mcbond_it 1.068 r_angle_other_deg 0.928 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1942 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 20
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement XDS data reduction