7LNG

TNA 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, SITTING DROP7.52930.1 M HEPES sodium pH 7.5, 1.5 M Lithium sulfate monohydrate
Crystal Properties
Matthews coefficientSolvent content
2.2745.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.165α = 90
b = 45.165β = 90
c = 82.831γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray99PIXELDECTRIS EIGER X 16M2021-02-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.033175APS23-ID-B

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
12.282.8399.680.1030.1110.040.996208.9532557.59
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)
12.22.241000.2950.3120.1010.9551.3

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 REPLACEMENTTHROUGHOUT5UEE2.282.83532429099.6630.2280.2250.274755.478
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]
-0.556-0.5561.112
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it8.328
r_lrange_other8.324
r_scangle_it6.744
r_scangle_other6.742
r_scbond_it5.028
r_scbond_other5.025
r_angle_other_deg4.041
r_angle_refined_deg2.663
r_chiral_restr_other1.885
r_symmetry_xyhbond_nbd_refined0.374
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it8.328
r_lrange_other8.324
r_scangle_it6.744
r_scangle_other6.742
r_scbond_it5.028
r_scbond_other5.025
r_angle_other_deg4.041
r_angle_refined_deg2.663
r_chiral_restr_other1.885
r_symmetry_xyhbond_nbd_refined0.374
r_nbtor_refined0.249
r_symmetry_nbd_other0.229
r_symmetry_nbtor_other0.228
r_nbd_other0.211
r_chiral_restr0.194
r_symmetry_nbd_refined0.178
r_nbd_refined0.133
r_xyhbond_nbd_refined0.117
r_symmetry_xyhbond_nbd_other0.028
r_bond_other_d0.025
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms378
Solvent Atoms
Heterogen Atoms318

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing