7LNE

ANA 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 DROP2931.7 M Lithium sulfate, 10 % w/v Glycerol
Crystal Properties
Matthews coefficientSolvent content
2.6653.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.408α = 90
b = 43.408β = 90
c = 86.554γ = 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
11.535098.70.0660.0730.0310.99919.95.814626
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)
11.531.5696.90.1980.2260.1060.9736.13.4

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 REPLACEMENTTHROUGHOUT5UEE1.5337.6211454775698.1510.1930.19130.225416.202
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]
-0.001-0.001-0.0010.005
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it4.882
r_lrange_other4.804
r_angle_other_deg3.85
r_scangle_it3.16
r_angle_refined_deg3.091
r_scangle_other3.05
r_scbond_it2.141
r_scbond_other2.044
r_chiral_restr_other1.751
r_chiral_restr0.505
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it4.882
r_lrange_other4.804
r_angle_other_deg3.85
r_scangle_it3.16
r_angle_refined_deg3.091
r_scangle_other3.05
r_scbond_it2.141
r_scbond_other2.044
r_chiral_restr_other1.751
r_chiral_restr0.505
r_symmetry_nbtor_other0.3
r_symmetry_xyhbond_nbd_refined0.258
r_nbtor_refined0.252
r_nbd_other0.247
r_symmetry_nbd_other0.212
r_xyhbond_nbd_refined0.206
r_symmetry_nbd_refined0.176
r_nbd_refined0.156
r_bond_other_d0.033
r_bond_refined_d0.025
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 Atoms101
Heterogen Atoms332

Software

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