7LNF

3'-deoxy 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 DROP62930.02 M Magnesium sulfate hydrate, 0.002 M Cobalt (II) chloride hexahydrate, 0.05 M Sodium cacodylate trihydrate pH 6.0, 25% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.0005 M Spermine
Crystal Properties
Matthews coefficientSolvent content
2.9858.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.822α = 90
b = 46.822β = 90
c = 83.199γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray99CCDADSC QUANTUM 315r2020-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21ALS8.2.2

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
11.655099.80.0840.090.03123.11013195
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)
11.651.6899.40.3930.4180.1420.9874.58

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 REPLACEMENTTHROUGHOUT5UEE1.65227.7481179055389.0080.210.20810.239415.582
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]
-0.002-0.001-0.0020.006
RMS Deviations
KeyRefinement Restraint Deviation
r_angle_other_deg4.099
r_lrange_it3.845
r_lrange_other3.694
r_angle_refined_deg2.876
r_scangle_it2.275
r_scangle_other2.274
r_scbond_it1.891
r_scbond_other1.89
r_chiral_restr_other1.883
r_chiral_restr0.461
RMS Deviations
KeyRefinement Restraint Deviation
r_angle_other_deg4.099
r_lrange_it3.845
r_lrange_other3.694
r_angle_refined_deg2.876
r_scangle_it2.275
r_scangle_other2.274
r_scbond_it1.891
r_scbond_other1.89
r_chiral_restr_other1.883
r_chiral_restr0.461
r_symmetry_nbtor_other0.275
r_nbtor_refined0.251
r_xyhbond_nbd_refined0.241
r_symmetry_xyhbond_nbd_refined0.209
r_symmetry_nbd_other0.205
r_nbd_other0.192
r_nbd_refined0.086
r_symmetry_nbd_refined0.082
r_bond_other_d0.031
r_bond_refined_d0.025
r_gen_planes_refined0.016
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms378
Solvent Atoms123
Heterogen Atoms330

Software

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