1XR7

Crystal structure of RNA-dependent RNA Polymerase 3D from human rhinovirus serotype 16


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6286ammonium sulfate, citrate, AMPPNP, MgCl2 or MnCl2, pH 5.60, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Crystal Properties
Matthews coefficientSolvent content
2.8557

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.976α = 90
b = 100.955β = 90
c = 116.839γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.11.0ALS5.0.1

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
12.3200.0740.074155.25317753177
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)
2.32.4990.3420.3425.55

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.3205037150371270099.290.256640.254420.29702RANDOM28.106
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]
1.8-0.49-1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.872
r_dihedral_angle_4_deg24.302
r_dihedral_angle_1_deg5.582
r_scangle_it1.846
r_angle_refined_deg1.114
r_scbond_it1.07
r_mcangle_it0.899
r_angle_other_deg0.795
r_mcbond_it0.471
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.872
r_dihedral_angle_4_deg24.302
r_dihedral_angle_1_deg5.582
r_scangle_it1.846
r_angle_refined_deg1.114
r_scbond_it1.07
r_mcangle_it0.899
r_angle_other_deg0.795
r_mcbond_it0.471
r_nbtor_refined0.303
r_nbd_other0.214
r_symmetry_vdw_other0.214
r_nbd_refined0.18
r_symmetry_hbond_refined0.177
r_symmetry_vdw_refined0.15
r_xyhbond_nbd_refined0.138
r_nbtor_other0.085
r_chiral_restr0.068
r_bond_refined_d0.008
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_refined
r_metal_ion_other
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 Atoms7364
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement