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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 Z952016136 (DNV2_NS5A-x0323)
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 2.44 49.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.525 α = 90 b = 117.36 β = 90 c = 148.89 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 2023-11-30 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 2.43 46.08 99.9 0.381 0.396 0.107 0.991 5.7 13.5 27513
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 2.43 2.52 98.8 3.804 3.95 1.058 0.342 13.8
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 2.43 46.13 26048 1405 99.61 0.20364 0.19934 0.2193 0.281 0.2826 RANDOM 68.646
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] -1.99 -1.64 3.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.118 r_dihedral_angle_3_deg 18.772 r_dihedral_angle_4_deg 18.066 r_long_range_B_other 17.991 r_long_range_B_refined 17.956 r_mcangle_other 7.621 r_mcangle_it 7.618 r_scangle_other 7.521 r_dihedral_angle_1_deg 7.049 r_mcbond_other 4.528
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.118 r_dihedral_angle_3_deg 18.772 r_dihedral_angle_4_deg 18.066 r_long_range_B_other 17.991 r_long_range_B_refined 17.956 r_mcangle_other 7.621 r_mcangle_it 7.618 r_scangle_other 7.521 r_dihedral_angle_1_deg 7.049 r_mcbond_other 4.528 r_mcbond_it 4.51 r_scbond_it 4.413 r_scbond_other 4.413 r_angle_refined_deg 1.438 r_angle_other_deg 1.167 r_chiral_restr 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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 452 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement REFMAC5 refinement Aimless data scaling PHASER phasing XDS data reduction