3FRZ

Crystal Structure of HCV NS5B RNA polymerase in complex with PF868554


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5298Stock crystals generated from 2uL Protein:AG9322(1:5)+ 2uL precipitant equilibrated against reservoir 18.0% PEG 3K, 0.1M Citrate pH 5.5, 14% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.2α = 90
b = 83.2β = 90
c = 180.263γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray101IMAGE PLATEMAR scanner 345 mm plateOSMIC CONFOCAL OPTICS2004-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-D1.5418

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
11.861097.40.03311.985231152311
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)
1.861.9395.30.20513.411.95021

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.86105231149603266297.470.177260.174870.2214RANDOM26.046
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]
-0.11-0.110.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.516
r_scangle_it4.035
r_scbond_it2.617
r_mcangle_it1.661
r_angle_refined_deg1.482
r_mcbond_it0.913
r_angle_other_deg0.857
r_nbd_other0.25
r_symmetry_vdw_other0.235
r_nbd_refined0.212
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.516
r_scangle_it4.035
r_scbond_it2.617
r_mcangle_it1.661
r_angle_refined_deg1.482
r_mcbond_it0.913
r_angle_other_deg0.857
r_nbd_other0.25
r_symmetry_vdw_other0.235
r_nbd_refined0.212
r_symmetry_hbond_refined0.197
r_symmetry_vdw_refined0.158
r_xyhbond_nbd_refined0.148
r_chiral_restr0.095
r_nbtor_other0.085
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4325
Nucleic Acid Atoms
Solvent Atoms660
Heterogen Atoms69

Software

Software
Software NamePurpose
MAR345dtbdata collection
ARP/wARPmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling