7I2Q | pdb_00007i2q

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 Z26333434 (DNV2_NS5A-x0693)


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
2.3848.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.609α = 90
b = 116.009β = 90
c = 146.707γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2023-12-05SINGLE 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
12.2649.61000.3820.3970.1070.994513.633430
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)
12.262.3399.65.7025.9151.5620.41914

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.2649.631182168198.20.246290.242650.35420.311670.3699RANDOM80.308
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]
-4.68-1.456.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.678
r_dihedral_angle_3_deg15.821
r_dihedral_angle_4_deg13.282
r_long_range_B_refined12.565
r_long_range_B_other12.536
r_mcangle_it5.677
r_mcangle_other5.677
r_dihedral_angle_1_deg5.409
r_scangle_other5.331
r_mcbond_other2.827
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.678
r_dihedral_angle_3_deg15.821
r_dihedral_angle_4_deg13.282
r_long_range_B_refined12.565
r_long_range_B_other12.536
r_mcangle_it5.677
r_mcangle_other5.677
r_dihedral_angle_1_deg5.409
r_scangle_other5.331
r_mcbond_other2.827
r_mcbond_it2.771
r_scbond_other2.553
r_scbond_it2.552
r_angle_refined_deg1.253
r_angle_other_deg1.079
r_chiral_restr0.042
r_bond_refined_d0.004
r_gen_planes_refined0.004
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 Atoms4688
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction