7HKM

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 Z851110644 (DNV2_NS5A-x0288)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293.15350 mM Magnesium chloride, 10% PEG 4000, 100 mM MES, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.4249.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.445α = 90
b = 116.793β = 90
c = 148.624γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2023-08-09SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92124DiamondI04-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6349.911000.1350.140.0380.99910.413.189546
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)RedundancyNumber Unique Reflections (All)
11.631.6699.65.2335.5121.7190.33610.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5K5M1.6349.9682331443596.850.195740.194210.22338RANDOM47.267
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]
-2.120.711.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.964
r_dihedral_angle_4_deg17.013
r_dihedral_angle_3_deg16.574
r_long_range_B_refined8.679
r_long_range_B_other8.632
r_dihedral_angle_1_deg6.603
r_scangle_other6.104
r_mcangle_it5.391
r_mcangle_other5.391
r_scbond_it3.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.964
r_dihedral_angle_4_deg17.013
r_dihedral_angle_3_deg16.574
r_long_range_B_refined8.679
r_long_range_B_other8.632
r_dihedral_angle_1_deg6.603
r_scangle_other6.104
r_mcangle_it5.391
r_mcangle_other5.391
r_scbond_it3.78
r_scbond_other3.78
r_mcbond_other3.341
r_mcbond_it3.334
r_angle_refined_deg1.474
r_angle_other_deg1.291
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms4759
Nucleic Acid Atoms
Solvent Atoms457
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction