1XR5

Crystal Structure of the RNA-dependent RNA Polymerase 3D from human rhinovirus serotype 14


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7286sodium formate, glycerol, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Crystal Properties
Matthews coefficientSolvent content
3.9470

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.326α = 90
b = 97.326β = 90
c = 153.113γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.844APS17-ID

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
12.8990.1020.102155.33607336073
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)
2.82.9320.410.411.31.5

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 DIFFRACTIONSADTHROUGHOUT2.8201861518615100892.670.26650.265080.29275RANDOM57.69
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]
2.051.032.05-3.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.804
r_dihedral_angle_4_deg18.663
r_dihedral_angle_1_deg6.102
r_scangle_it1.782
r_angle_other_deg1.229
r_angle_refined_deg1.223
r_mcangle_it0.976
r_scbond_it0.963
r_mcbond_it0.512
r_nbtor_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.804
r_dihedral_angle_4_deg18.663
r_dihedral_angle_1_deg6.102
r_scangle_it1.782
r_angle_other_deg1.229
r_angle_refined_deg1.223
r_mcangle_it0.976
r_scbond_it0.963
r_mcbond_it0.512
r_nbtor_refined0.322
r_nbd_other0.221
r_nbd_refined0.209
r_symmetry_vdw_other0.193
r_xyhbond_nbd_refined0.161
r_symmetry_vdw_refined0.147
r_nbtor_other0.087
r_metal_ion_refined0.08
r_chiral_restr0.064
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
r_dihedral_angle_3_deg
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3678
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms1

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMACrefinement