2HCN

Crystal structure of RNA dependent RNA polymerase domain from west nile virus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HCSWEST NILE VIRUS RNA DEPENDANT RNA POLYMERASE COORDINATES 2HCS (DOMAIN FROM AMINO ACIDS 317-905)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829310% peg 8000, Imid 0.1M, Ca(OAc)2 0.2M, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0459.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.064α = 90
b = 110.064β = 90
c = 68.572γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2005-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-30.9330ESRFID14-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.356999.90.05521.85.73433861.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.4899.70.561.53.54930

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTWEST NILE VIRUS RNA DEPENDANT RNA POLYMERASE COORDINATES 2HCS (DOMAIN FROM AMINO ACIDS 317-905)2.3534.823434832583173499.920.209620.209620.207010.25944RANDOM58.568
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]
-1.96-1.963.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.388
r_dihedral_angle_3_deg20.655
r_dihedral_angle_4_deg19.044
r_dihedral_angle_1_deg7.286
r_scangle_it2.747
r_scbond_it1.827
r_angle_refined_deg1.729
r_mcangle_it1.255
r_mcbond_it0.728
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.388
r_dihedral_angle_3_deg20.655
r_dihedral_angle_4_deg19.044
r_dihedral_angle_1_deg7.286
r_scangle_it2.747
r_scbond_it1.827
r_angle_refined_deg1.729
r_mcangle_it1.255
r_mcbond_it0.728
r_nbtor_refined0.302
r_symmetry_vdw_refined0.257
r_nbd_refined0.216
r_symmetry_hbond_refined0.214
r_xyhbond_nbd_refined0.181
r_chiral_restr0.151
r_metal_ion_refined0.022
r_bond_refined_d0.021
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3931
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
AMoREphasing