2J7U

Dengue virus NS5 RNA dependent RNA polymerase domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HFZPDB ENTRY 2HFZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.50.1 M TRIS-HCL PH 8.5, 0.8M K/NA TARTRATE, 0.5% W/V PEG MME 5K.
Crystal Properties
Matthews coefficientSolvent content
2.9958.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.15α = 90
b = 180.478β = 90
c = 57.987γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2006-09-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.854899.90.0114.624.972065
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9399.90.542.984.9

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2HFZ1.852068360364699.90.2010.20.234RANDOM36.72
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]
-0.972.23-1.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.979
r_dihedral_angle_4_deg15.995
r_dihedral_angle_3_deg13.633
r_dihedral_angle_1_deg4.59
r_scangle_it1.487
r_scbond_it0.92
r_angle_refined_deg0.919
r_mcangle_it0.602
r_mcbond_it0.351
r_nbtor_refined0.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.979
r_dihedral_angle_4_deg15.995
r_dihedral_angle_3_deg13.633
r_dihedral_angle_1_deg4.59
r_scangle_it1.487
r_scbond_it0.92
r_angle_refined_deg0.919
r_mcangle_it0.602
r_mcbond_it0.351
r_nbtor_refined0.296
r_symmetry_vdw_refined0.176
r_nbd_refined0.175
r_symmetry_hbond_refined0.141
r_xyhbond_nbd_refined0.11
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4642
Nucleic Acid Atoms
Solvent Atoms505
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
AMoREphasing