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VirC mutant C114A-Q334A-R335A-R338A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 11% PEG 3350, 12.5% 2-methyl-2,4-pentanediol, 100 mM amino acids (0.02 M DL-glutamic acid monohydrate, 0.02 M glycine, 0.02 M DL-serine, 0.02 M DL-alanine, 0.2 M DL-lysine monohydrochloride), 100 mM MES-imidazole buffer, pH 6.5.
Crystal Properties Matthews coefficient Solvent content 2.7 54.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.35 α = 90 b = 126.35 β = 90 c = 324.94 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 80 PIXEL DECTRIS EIGER X 9M 2019-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980112195015 SOLEIL PROXIMA 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 1.99 45.42 99.2 0.145 0.147 0.023 0.999 22.6 39.6 68537
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 1.99 2.04 96 1.551 1.57 0.245 0.859 39
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 1.99 45.42 65110 3427 99.06 0.1738 0.17208 0.174 0.20644 0.2089 RANDOM 32.641
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.432 r_dihedral_angle_4_deg 18.588 r_dihedral_angle_3_deg 13.524 r_dihedral_angle_1_deg 7.071 r_long_range_B_refined 6.286 r_long_range_B_other 6.258 r_scangle_other 5.272 r_scbond_it 3.674 r_scbond_other 3.674 r_mcangle_other 3.576
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.432 r_dihedral_angle_4_deg 18.588 r_dihedral_angle_3_deg 13.524 r_dihedral_angle_1_deg 7.071 r_long_range_B_refined 6.286 r_long_range_B_other 6.258 r_scangle_other 5.272 r_scbond_it 3.674 r_scbond_other 3.674 r_mcangle_other 3.576 r_mcangle_it 3.571 r_mcbond_it 2.786 r_mcbond_other 2.756 r_angle_refined_deg 1.759 r_angle_other_deg 1.44 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 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 6031 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing