7KUP

2'-OMe 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
2.8556.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.972α = 90
b = 48.972β = 90
c = 82.204γ = 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
11.445099.90.0850.0870.020.98826.118.721287
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)
11.441.4699.90.4970.5120.1220.9855.115.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5UEE1.44501861188987.4130.20.19860.218215.913
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]
0.0010.0010.001-0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it4.568
r_lrange_other4.209
r_angle_other_deg3.62
r_angle_refined_deg3.208
r_scangle_it3.038
r_scangle_other3.038
r_scbond_it2.182
r_scbond_other2.181
r_chiral_restr_other1.723
r_symmetry_xyhbond_nbd_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it4.568
r_lrange_other4.209
r_angle_other_deg3.62
r_angle_refined_deg3.208
r_scangle_it3.038
r_scangle_other3.038
r_scbond_it2.182
r_scbond_other2.181
r_chiral_restr_other1.723
r_symmetry_xyhbond_nbd_refined0.303
r_symmetry_nbtor_other0.286
r_nbtor_refined0.247
r_xyhbond_nbd_refined0.221
r_symmetry_nbd_other0.206
r_nbd_other0.171
r_chiral_restr0.138
r_symmetry_nbd_refined0.119
r_nbd_refined0.087
r_bond_other_d0.031
r_bond_refined_d0.028
r_gen_planes_refined0.023
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms378
Solvent Atoms148
Heterogen Atoms332

Software

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