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X-ray crystal structure of an engineered Viperin-like enzyme from T. virens with bound CTP and SAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7N7I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.1 M HEPES (pH 7.0), 10% (w/v) PEG 6K
Crystal Properties Matthews coefficient Solvent content 2.12 41.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.131 α = 90 b = 85.131 β = 90 c = 110.471 γ = 120
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 EIGER X 16M 2022-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.9793 NSLS-II 17-ID-2
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 1.677 61.323 100 0.152 0.17 0.076 0.997 9 9.8 102720
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 1.677 1.705 2.332 2.612 1.167 0.358 1
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 1.677 19.86 97622 4939 99.9 0.15675 0.1552 0.1648 0.18793 0.1952 RANDOM 26.96
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] 0.37 0.18 0.37 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.296 r_dihedral_angle_3_deg 14.437 r_dihedral_angle_4_deg 13.768 r_dihedral_angle_1_deg 7.06 r_long_range_B_refined 6.424 r_long_range_B_other 6.34 r_scangle_other 5.272 r_scbond_it 3.469 r_scbond_other 3.461 r_mcangle_it 3.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.296 r_dihedral_angle_3_deg 14.437 r_dihedral_angle_4_deg 13.768 r_dihedral_angle_1_deg 7.06 r_long_range_B_refined 6.424 r_long_range_B_other 6.34 r_scangle_other 5.272 r_scbond_it 3.469 r_scbond_other 3.461 r_mcangle_it 3.063 r_mcangle_other 3.063 r_mcbond_it 2.185 r_mcbond_other 2.185 r_angle_refined_deg 1.575 r_angle_other_deg 1.411 r_chiral_restr 0.119 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 6920 Nucleic Acid Atoms Solvent Atoms 710 Heterogen Atoms 231
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing