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Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z3765495818 (DNV2_NS5A-x0825)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K5M 5K5M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 350 mM Magnesium chloride, 10% PEG 4000, 100 mM MES, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.39 48.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.014 α = 90 b = 116.51 β = 90 c = 148.14 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 PIXEL DECTRIS EIGER2 XE 9M 2023-12-05 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92124 Diamond I04-1
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 1.82 91.59 99.8 0.189 0.196 0.053 0.998 7.9 13.7 63874
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 1.82 1.86 97.3 4.169 4.326 1.153 0.336 14
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5K5M 1.82 91.58 60250 3277 99.23 0.2038 0.2016 0.2234 0.24307 0.2537 RANDOM 49.636
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] -2.05 -0.04 2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.57 r_dihedral_angle_4_deg 18.33 r_dihedral_angle_3_deg 17.502 r_long_range_B_refined 8.952 r_long_range_B_other 8.796 r_dihedral_angle_1_deg 6.581 r_scangle_other 5.241 r_mcangle_other 4.945 r_mcangle_it 4.936 r_scbond_it 3.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.57 r_dihedral_angle_4_deg 18.33 r_dihedral_angle_3_deg 17.502 r_long_range_B_refined 8.952 r_long_range_B_other 8.796 r_dihedral_angle_1_deg 6.581 r_scangle_other 5.241 r_mcangle_other 4.945 r_mcangle_it 4.936 r_scbond_it 3.122 r_scbond_other 3.122 r_mcbond_other 2.962 r_mcbond_it 2.924 r_angle_refined_deg 1.394 r_angle_other_deg 1.211 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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 4752 Nucleic Acid Atoms Solvent Atoms 447 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement REFMAC5 refinement Aimless data scaling PHASER phasing XDS data reduction