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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 Z415636694 (DNV2_NS5A-x0843)
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 2.37 48.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.312 α = 90 b = 115.777 β = 90 c = 146.816 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 1.76 73.41 99.9 0.184 0.191 0.051 0.998 7.1 13.6 69526
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 1.76 1.8 98.8 5.518 5.751 1.605 0.309 12.7
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 1.76 73.41 61302 3335 92.81 0.21651 0.21428 0.2781 0.2562 0.3024 RANDOM 61.296
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] -3.08 3.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.669 r_dihedral_angle_3_deg 15.744 r_dihedral_angle_4_deg 15.554 r_long_range_B_refined 10.125 r_long_range_B_other 10.026 r_dihedral_angle_1_deg 6.302 r_scangle_other 6.275 r_mcangle_it 5.72 r_mcangle_other 5.72 r_scbond_it 3.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.669 r_dihedral_angle_3_deg 15.744 r_dihedral_angle_4_deg 15.554 r_long_range_B_refined 10.125 r_long_range_B_other 10.026 r_dihedral_angle_1_deg 6.302 r_scangle_other 6.275 r_mcangle_it 5.72 r_mcangle_other 5.72 r_scbond_it 3.682 r_scbond_other 3.682 r_mcbond_other 3.271 r_mcbond_it 3.204 r_angle_refined_deg 1.441 r_angle_other_deg 1.201 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 4671 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction