2PGG

Crystal Structure of a Birnavirus (IBDV) RNA-dependent RNA Polymerase VP1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293100mM HEPES, 1.3M sodium malonate, 10mM sodium iodide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.4672.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.103α = 90
b = 122.103β = 90
c = 359.017γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Osmic mirror2004-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
12.54096.40.06530.75.7558715381939.9
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)
2.52.5972.70.3384.534.85462

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 DIFFRACTIONMIRASTHROUGHOUT2.539.975381953744326796.30.2160.2160.254RANDOM49.2
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]
0.484.980.48-0.97
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.8
c_scangle_it3.2
c_mcangle_it2.44
c_scbond_it2.15
c_mcbond_it1.44
c_angle_deg1.3
c_improper_angle_d0.83
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.8
c_scangle_it3.2
c_mcangle_it2.44
c_scbond_it2.15
c_mcbond_it1.44
c_angle_deg1.3
c_improper_angle_d0.83
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6020
Nucleic Acid Atoms
Solvent Atoms427
Heterogen Atoms

Software

Software
Software NamePurpose
CNSrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing