5UEE

RNA primer-template complex with guanosine dinucleotide ligand G(5')ppp(5')G


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DHC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.05 M Magnesium chloride, 0.1 M Imidazole pH 6.5, 1.0 M Sodium acetate trihydrate
Crystal Properties
Matthews coefficientSolvent content
2.9458.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.964α = 90
b = 46.964β = 90
c = 83.103γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray99CCDADSC QUANTUM 3152016-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.20.997ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.95099.40.0630.97935.39.18742
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9794.40.4640.9021.864.5

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 REPLACEMENTTHROUGHOUT5dhc1.950829944299.270.234060.231970.27469RANDOM32.419
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]
0.010.010.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined5.839
r_long_range_B_other5.839
r_scangle_other4.173
r_angle_other_deg3.563
r_scbond_it3.18
r_scbond_other3.178
r_angle_refined_deg2.659
r_chiral_restr0.136
r_bond_other_d0.055
r_bond_refined_d0.021
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined5.839
r_long_range_B_other5.839
r_scangle_other4.173
r_angle_other_deg3.563
r_scbond_it3.18
r_scbond_other3.178
r_angle_refined_deg2.659
r_chiral_restr0.136
r_bond_other_d0.055
r_bond_refined_d0.021
r_gen_planes_refined0.017
r_gen_planes_other0.002
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms596
Solvent Atoms23
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing