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X-ray crystal structure of the 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 Bis-Tris pH 6.5, 0.2 M NaCl, 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2 38.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.569 α = 90 b = 80.309 β = 96.71 c = 105.613 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 EIGER X 16M 2022-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.9201 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 1.72 28.59 99.3 0.07 0.095 0.063 0.992 9.6 3.9 354684
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 1.72 1.75 0.445 0.587 0.377 0.87 2.7
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 1.72 28.59 85544 4454 99.1 0.26284 0.26133 0.2686 0.29231 0.2985 RANDOM 52.117
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] 0.93 -1.58 0.34 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.212 r_dihedral_angle_1_deg 7.104 r_dihedral_angle_2_deg 6.542 r_long_range_B_other 3.061 r_long_range_B_refined 3.054 r_scangle_other 2.101 r_mcangle_it 1.964 r_mcangle_other 1.964 r_angle_refined_deg 1.511 r_scbond_it 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.212 r_dihedral_angle_1_deg 7.104 r_dihedral_angle_2_deg 6.542 r_long_range_B_other 3.061 r_long_range_B_refined 3.054 r_scangle_other 2.101 r_mcangle_it 1.964 r_mcangle_other 1.964 r_angle_refined_deg 1.511 r_scbond_it 1.26 r_scbond_other 1.256 r_mcbond_it 1.141 r_mcbond_other 1.14 r_angle_other_deg 0.772 r_chiral_restr 0.103 r_bond_refined_d 0.011 r_gen_planes_other 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_dihedral_angle_4_deg 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 6743 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction PHASER phasing