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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 Z32327641 (DNV2_NS5A-x0781)
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 2.4 48.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.338 α = 90 b = 116.214 β = 90 c = 148.02 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 1.59 58.11 100 0.123 0.128 0.035 0.999 10.5 12.9 95224
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 1.59 1.62 99.8 3.512 3.71 1.184 0.37 9.6
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 1.59 58.11 89372 4790 98.81 0.20251 0.20112 0.2284 0.22761 0.2485 RANDOM 50.831
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] -2.18 0.23 1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.627 r_dihedral_angle_4_deg 16.957 r_dihedral_angle_3_deg 15.831 r_long_range_B_refined 12.495 r_long_range_B_other 12.475 r_dihedral_angle_1_deg 6.135 r_scangle_other 5.808 r_mcangle_it 4.873 r_mcangle_other 4.872 r_scbond_it 3.498
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.627 r_dihedral_angle_4_deg 16.957 r_dihedral_angle_3_deg 15.831 r_long_range_B_refined 12.495 r_long_range_B_other 12.475 r_dihedral_angle_1_deg 6.135 r_scangle_other 5.808 r_mcangle_it 4.873 r_mcangle_other 4.872 r_scbond_it 3.498 r_scbond_other 3.498 r_mcbond_other 2.942 r_mcbond_it 2.924 r_angle_refined_deg 1.497 r_angle_other_deg 1.27 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 4644 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction