4Y2A

Crystal Structure of Coxsackie Virus B3 3D polymerase in complex with GPC-N114 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DDK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29350 mM Tris pH 7.5, 24.5% (w/v) glycerol, 1.29 M ammonium sulfate.
Crystal Properties
Matthews coefficientSolvent content
3.7867.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.74α = 90
b = 74.74β = 90
c = 289.05γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2011-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.977ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.972.499.80.0810.087.63.618099
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.93.0599.50.4150.3573.8

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 REPLACEMENTTHROUGHOUT3DDK2.972.361809997999.660.200250.197610.25049RANDOM55.837
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]
3.513.51-7.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.027
r_dihedral_angle_3_deg18.418
r_dihedral_angle_4_deg17.838
r_long_range_B_refined9.819
r_long_range_B_other9.819
r_scangle_other7.4
r_dihedral_angle_1_deg6.648
r_mcangle_it5.802
r_mcangle_other5.802
r_scbond_it4.659
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.027
r_dihedral_angle_3_deg18.418
r_dihedral_angle_4_deg17.838
r_long_range_B_refined9.819
r_long_range_B_other9.819
r_scangle_other7.4
r_dihedral_angle_1_deg6.648
r_mcangle_it5.802
r_mcangle_other5.802
r_scbond_it4.659
r_scbond_other4.652
r_mcbond_it3.783
r_mcbond_other3.769
r_angle_refined_deg1.712
r_angle_other_deg1.072
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.007
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 Atoms3727
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing