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1.9 Angstrom Crystal Structure of NS5 Methyl Transferase from Dengue Virus 1 in Complex with S-Adenosylmethionine and Beta-D-Fructopyranose.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4V0Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 Protein: 6.8 mg/ml, 0.25M Sodium chloride, 0.1M Tris HCl (pH 8.3);
Screen: JCSG+ (E2), 0.2M Sodium chloride, 0.1M Sodium cacodylate (pH 6.5) 2M Ammonium sulfate;
Cryo: 4M Ammonium sulfate : 50% Sucrose (1:1).
Crystal Properties Matthews coefficient Solvent content 2.99 58.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.38 α = 90 b = 86.23 β = 90 c = 144.307 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD C(111) 2014-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.9 30 99.3 0.111 0.111 0.882 16.2 5.9 29015 -3 17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 100 0.641 3.9 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4V0Q 1.9 29.19 27572 1386 99.3 0.15449 0.15299 0.18422 0.1851 RANDOM 19.827
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] -1.13 -1.93 3.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.199 r_dihedral_angle_4_deg 10.945 r_dihedral_angle_3_deg 10.51 r_long_range_B_refined 7.079 r_long_range_B_other 6.683 r_dihedral_angle_1_deg 3.356 r_scangle_other 2.052 r_angle_refined_deg 1.505 r_scbond_it 1.278 r_scbond_other 1.275
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.199 r_dihedral_angle_4_deg 10.945 r_dihedral_angle_3_deg 10.51 r_long_range_B_refined 7.079 r_long_range_B_other 6.683 r_dihedral_angle_1_deg 3.356 r_scangle_other 2.052 r_angle_refined_deg 1.505 r_scbond_it 1.278 r_scbond_other 1.275 r_mcangle_it 1.108 r_mcangle_other 1.107 r_angle_other_deg 0.866 r_mcbond_it 0.64 r_mcbond_other 0.639 r_chiral_restr 0.09 r_gen_planes_refined 0.023 r_gen_planes_other 0.018 r_bond_refined_d 0.01 r_bond_other_d 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 2053 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MoRDa phasing