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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 Z68299550 (DNV2_NS5A-x0248)
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 2.42 49.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.596 α = 90 b = 116.532 β = 90 c = 148.449 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 2023-08-09 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 74.1 99.9 0.231 0.24 0.065 0.997 8.5 13.6 72558
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 97.3 13.129 13.721 3.931 0.12 12.3
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 1.75 74.34 67984 3680 98.68 0.19194 0.1901 0.2095 0.22522 0.2338 RANDOM 51.774
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] -2.31 0.24 2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.145 r_dihedral_angle_4_deg 18.876 r_dihedral_angle_3_deg 16.074 r_long_range_B_refined 9.555 r_long_range_B_other 9.458 r_dihedral_angle_1_deg 6.53 r_scangle_other 6.204 r_mcangle_other 5.598 r_mcangle_it 5.596 r_scbond_it 3.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.145 r_dihedral_angle_4_deg 18.876 r_dihedral_angle_3_deg 16.074 r_long_range_B_refined 9.555 r_long_range_B_other 9.458 r_dihedral_angle_1_deg 6.53 r_scangle_other 6.204 r_mcangle_other 5.598 r_mcangle_it 5.596 r_scbond_it 3.881 r_scbond_other 3.881 r_mcbond_other 3.549 r_mcbond_it 3.511 r_angle_refined_deg 1.468 r_angle_other_deg 1.261 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 4759 Nucleic Acid Atoms Solvent Atoms 455 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement REFMAC5 refinement Aimless data scaling PHASER phasing XDS data reduction