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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 Z48978335 (DNV2_NS5A-x1196)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K5M 5K5M
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 2.43 49.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.437 α = 90 b = 116.952 β = 90 c = 149.281 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 1.66 50.01 100 0.121 0.126 0.034 0.999 12.3 13.3 85258
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 1.66 1.69 99.6 3.838 4.036 1.228 0.35 10.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5K5M 1.66 50.07 80491 4340 99.42 0.19577 0.19423 0.2142 0.22368 0.2384 RANDOM 47.286
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] -2.22 0.95 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.951 r_dihedral_angle_4_deg 17.884 r_dihedral_angle_3_deg 16.478 r_long_range_B_refined 8.976 r_long_range_B_other 8.92 r_dihedral_angle_1_deg 6.386 r_scangle_other 6.11 r_mcangle_it 5.283 r_mcangle_other 5.282 r_scbond_it 3.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.951 r_dihedral_angle_4_deg 17.884 r_dihedral_angle_3_deg 16.478 r_long_range_B_refined 8.976 r_long_range_B_other 8.92 r_dihedral_angle_1_deg 6.386 r_scangle_other 6.11 r_mcangle_it 5.283 r_mcangle_other 5.282 r_scbond_it 3.828 r_scbond_other 3.828 r_mcbond_other 3.295 r_mcbond_it 3.281 r_angle_refined_deg 1.502 r_angle_other_deg 1.3 r_chiral_restr 0.072 r_bond_refined_d 0.009 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 4769 Nucleic Acid Atoms Solvent Atoms 446 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement REFMAC5 refinement Aimless data scaling PHASER phasing XDS data reduction