7HKQ

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 Z1203329531 (DNV2_NS5A-x0428)


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
2.3447.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.493α = 90
b = 115.52β = 90
c = 145.412γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2023-12-03SINGLE 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
12.1649.399.90.2880.2990.080.9976.413.637529
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)
12.162.2399.46.0296.2541.6510.34714.1

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 REPLACEMENTTHROUGHOUT5K5M2.1649.3734836187197.420.217050.213450.28107RANDOM73.457
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]
-4.40.264.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.852
r_dihedral_angle_4_deg19.558
r_dihedral_angle_3_deg17.953
r_long_range_B_refined12.056
r_long_range_B_other11.861
r_dihedral_angle_1_deg6.945
r_mcangle_other6.918
r_scangle_other6.916
r_mcangle_it6.912
r_mcbond_other4.165
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.852
r_dihedral_angle_4_deg19.558
r_dihedral_angle_3_deg17.953
r_long_range_B_refined12.056
r_long_range_B_other11.861
r_dihedral_angle_1_deg6.945
r_mcangle_other6.918
r_scangle_other6.916
r_mcangle_it6.912
r_mcbond_other4.165
r_mcbond_it4.117
r_scbond_it4.011
r_scbond_other4.01
r_angle_refined_deg1.353
r_angle_other_deg1.149
r_chiral_restr0.055
r_bond_refined_d0.005
r_gen_planes_refined0.005
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 Atoms4748
Nucleic Acid Atoms
Solvent Atoms423
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction