7KUO

FANA 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 DROP72932.4 M Sodium malonate pH 7.0, 50 mM Magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
2.8256.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.072α = 90
b = 49.072β = 90
c = 81.254γ = 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
12.28501000.1130.1170.1140.99929.218.85536
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)
12.282.321000.4910.5040.0270.9727.519.2

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 REPLACEMENTTHROUGHOUT5UEE2.28150553629899.9820.2070.20370.26327.55
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]
0.0120.0060.012-0.039
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it4.638
r_lrange_other4.529
r_angle_other_deg3.786
r_angle_refined_deg3.366
r_scangle_it3.247
r_scangle_other3.246
r_scbond_it2.296
r_scbond_other2.294
r_chiral_restr_other1.733
r_chiral_restr0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it4.638
r_lrange_other4.529
r_angle_other_deg3.786
r_angle_refined_deg3.366
r_scangle_it3.247
r_scangle_other3.246
r_scbond_it2.296
r_scbond_other2.294
r_chiral_restr_other1.733
r_chiral_restr0.52
r_symmetry_nbtor_other0.277
r_symmetry_xyhbond_nbd_refined0.262
r_nbtor_refined0.246
r_xyhbond_nbd_refined0.222
r_symmetry_nbd_other0.221
r_nbd_other0.177
r_symmetry_nbd_refined0.144
r_nbd_refined0.112
r_symmetry_xyhbond_nbd_other0.038
r_bond_other_d0.028
r_bond_refined_d0.027
r_gen_planes_refined0.014
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms378
Solvent Atoms47
Heterogen Atoms327

Software

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