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DENGUE 3 NS5 METHYLTRANSFERASE BOUND TO S-Adenosyl-L-homocysteine and Caffeic acid phenethyl ester
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R8R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 25% PEG 8000 100 mM Tris 200 mM NaCl 20 mM Trisodium citrate
Crystal Properties Matthews coefficient Solvent content 2.4122386 49.041695
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.648 α = 90 b = 60.722 β = 90 c = 184.36 γ = 90
Symmetry Space Group P 2 21 21
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 RIGAKU HyPix-6000HE 2023-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.6 23.056 98.6 0.188 7.3 6 108535
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.72 99.3 0.421
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4R8R 2.6 23.056 108535 924 99.328 0.233 0.231 0.2323 0.2727 0.2739 28.803
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] -2.711 -2.122 4.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.516 r_dihedral_angle_4_deg 18.661 r_dihedral_angle_3_deg 18.259 r_lrange_it 7.097 r_dihedral_angle_1_deg 5.843 r_scangle_it 3.32 r_mcangle_it 2.489 r_scbond_it 2.136 r_angle_refined_deg 1.558 r_mcbond_it 1.501
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.516 r_dihedral_angle_4_deg 18.661 r_dihedral_angle_3_deg 18.259 r_lrange_it 7.097 r_dihedral_angle_1_deg 5.843 r_scangle_it 3.32 r_mcangle_it 2.489 r_scbond_it 2.136 r_angle_refined_deg 1.558 r_mcbond_it 1.501 r_ext_dist_refined_d 0.337 r_nbtor_refined 0.312 r_symmetry_nbd_refined 0.28 r_symmetry_xyhbond_nbd_refined 0.265 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.149 r_ncsr_local_group_1 0.117 r_chiral_restr 0.097 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4086 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing