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Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- PanDDA analysis group deposition of ground-state model
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 49.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.485 α = 90 b = 116.856 β = 90 c = 148.568 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 2024-11-30 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) 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 1.5 74.38 100 0.085 1 13.2 112833
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 99.3 3.12 0.35 5605
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5K5M 1.5 74.39 107112 5721 98.43 0.1943 0.1928 0.2202 0.2078 RANDOM 41.292
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] -1.56 0.45 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.583 r_dihedral_angle_4_deg 18.973 r_dihedral_angle_3_deg 15.835 r_dihedral_angle_1_deg 6.284 r_mcangle_it 5.335 r_mcbond_it 3.566 r_mcbond_other 3.56 r_angle_refined_deg 1.576 r_angle_other_deg 1.365 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.583 r_dihedral_angle_4_deg 18.973 r_dihedral_angle_3_deg 15.835 r_dihedral_angle_1_deg 6.284 r_mcangle_it 5.335 r_mcbond_it 3.566 r_mcbond_other 3.56 r_angle_refined_deg 1.576 r_angle_other_deg 1.365 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4759 Nucleic Acid Atoms Solvent Atoms 457 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction