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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 Z1639162606 (DNV2_NS5A-x0567)
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 48.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.364 α = 90 b = 115.808 β = 90 c = 147.054 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 2023-12-02 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 1.78 73.55 99.9 0.17 0.177 0.048 0.999 9.1 13.7 67449
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 1.78 1.82 98.7 6.803 7.068 1.909 0.351 13.5
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 1.78 73.55 62747 3410 97.95 0.19814 0.19607 0.261 0.23523 0.2794 RANDOM 62.227
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] -2.69 -0.24 2.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.119 r_dihedral_angle_4_deg 16.474 r_dihedral_angle_3_deg 16.347 r_long_range_B_refined 9.069 r_long_range_B_other 8.914 r_dihedral_angle_1_deg 5.746 r_scangle_other 5.565 r_mcangle_it 5.277 r_mcangle_other 5.276 r_scbond_it 3.045
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.119 r_dihedral_angle_4_deg 16.474 r_dihedral_angle_3_deg 16.347 r_long_range_B_refined 9.069 r_long_range_B_other 8.914 r_dihedral_angle_1_deg 5.746 r_scangle_other 5.565 r_mcangle_it 5.277 r_mcangle_other 5.276 r_scbond_it 3.045 r_scbond_other 3.045 r_mcbond_other 2.806 r_mcbond_it 2.763 r_angle_refined_deg 1.333 r_angle_other_deg 1.192 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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 4685 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction