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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 POB0015 (DNV2_NS5A-x0866)
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 48.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.298 α = 90 b = 116.048 β = 90 c = 147.893 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 2023-12-06 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 1.75 91.3 99.9 0.327 0.34 0.091 0.998 8.2 13.7 71456
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 1.75 1.78 98.5 9.999 11.546 3.248 0.315 12.5
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 1.75 91.3 67114 3625 98.88 0.20323 0.20122 0.2411 0.2394 0.2615 RANDOM 57.528
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] -2.5 0.04 2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.945 r_dihedral_angle_4_deg 17.054 r_dihedral_angle_3_deg 16.646 r_long_range_B_refined 7.956 r_long_range_B_other 7.79 r_dihedral_angle_1_deg 6.05 r_scangle_other 4.912 r_mcangle_other 4.593 r_mcangle_it 4.592 r_scbond_it 2.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.945 r_dihedral_angle_4_deg 17.054 r_dihedral_angle_3_deg 16.646 r_long_range_B_refined 7.956 r_long_range_B_other 7.79 r_dihedral_angle_1_deg 6.05 r_scangle_other 4.912 r_mcangle_other 4.593 r_mcangle_it 4.592 r_scbond_it 2.762 r_scbond_other 2.762 r_mcbond_it 2.461 r_mcbond_other 2.461 r_angle_refined_deg 1.374 r_angle_other_deg 1.19 r_chiral_restr 0.058 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 4666 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction