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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 Z26333434 (DNV2_NS5A-x0693)
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 2.38 48.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.609 α = 90 b = 116.009 β = 90 c = 146.707 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 2.26 49.6 100 0.382 0.397 0.107 0.994 5 13.6 33430
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 2.26 2.33 99.6 5.702 5.915 1.562 0.419 14
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 2.26 49.6 31182 1681 98.2 0.24629 0.24265 0.3542 0.31167 0.3699 RANDOM 80.308
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] -4.68 -1.45 6.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.678 r_dihedral_angle_3_deg 15.821 r_dihedral_angle_4_deg 13.282 r_long_range_B_refined 12.565 r_long_range_B_other 12.536 r_mcangle_it 5.677 r_mcangle_other 5.677 r_dihedral_angle_1_deg 5.409 r_scangle_other 5.331 r_mcbond_other 2.827
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.678 r_dihedral_angle_3_deg 15.821 r_dihedral_angle_4_deg 13.282 r_long_range_B_refined 12.565 r_long_range_B_other 12.536 r_mcangle_it 5.677 r_mcangle_other 5.677 r_dihedral_angle_1_deg 5.409 r_scangle_other 5.331 r_mcbond_other 2.827 r_mcbond_it 2.771 r_scbond_other 2.553 r_scbond_it 2.552 r_angle_refined_deg 1.253 r_angle_other_deg 1.079 r_chiral_restr 0.042 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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 4688 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction