7KUM

LNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62930.1 M Sodium acetate trihydrate pH 4.6, 2.0 M Sodium formate, 50 mM Magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
2.7755.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.769α = 90
b = 47.769β = 90
c = 84.122γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray99PIXELDECTRIS PILATUS3 6M2020-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.977408ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.71501000.0520.0540.0130.99452.318.812474
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.711.740.4750.4890.1150.9946.917.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5UEE1.714501170161193.8330.2060.20520.220215.717
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]
-0.005-0.003-0.0050.018
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it5.342
r_lrange_other5.103
r_angle_other_deg3.9
r_angle_refined_deg3.048
r_scangle_it2.842
r_scangle_other2.841
r_scbond_it2.187
r_scbond_other2.185
r_chiral_restr_other1.779
r_xyhbond_nbd_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it5.342
r_lrange_other5.103
r_angle_other_deg3.9
r_angle_refined_deg3.048
r_scangle_it2.842
r_scangle_other2.841
r_scbond_it2.187
r_scbond_other2.185
r_chiral_restr_other1.779
r_xyhbond_nbd_refined0.305
r_symmetry_nbtor_other0.292
r_nbtor_refined0.245
r_symmetry_nbd_other0.22
r_symmetry_xyhbond_nbd_refined0.181
r_nbd_other0.172
r_nbd_refined0.168
r_chiral_restr0.135
r_symmetry_nbd_refined0.08
r_symmetry_xyhbond_nbd_other0.041
r_bond_other_d0.032
r_bond_refined_d0.027
r_gen_planes_refined0.019
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms378
Solvent Atoms115
Heterogen Atoms328

Software

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