7KUL

DNA 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 DROP6.52930.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 50 mM Magnesium Chloride
Crystal Properties
Matthews coefficientSolvent content
3.0554.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.443α = 90
b = 47.443β = 90
c = 82.803γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray99CCDADSC QUANTUM 315r2020-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.00ALS8.2.1

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
11.6450990.0750.0790.0260.98524.99.613719
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)
11.641.6797.40.3140.3390.1230.9895.35.4

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 REPLACEMENTTHROUGHOUT5UEE1.64501211656987.5810.210.20790.24718.93
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]
0.0010.0010.001-0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it4.73
r_lrange_other4.501
r_angle_other_deg3.84
r_scangle_it2.94
r_scangle_other2.939
r_angle_refined_deg2.88
r_scbond_it2.091
r_scbond_other2.09
r_chiral_restr_other1.816
r_chiral_restr0.481
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it4.73
r_lrange_other4.501
r_angle_other_deg3.84
r_scangle_it2.94
r_scangle_other2.939
r_angle_refined_deg2.88
r_scbond_it2.091
r_scbond_other2.09
r_chiral_restr_other1.816
r_chiral_restr0.481
r_nbtor_refined0.252
r_symmetry_nbtor_other0.244
r_symmetry_nbd_other0.222
r_nbd_other0.169
r_xyhbond_nbd_refined0.166
r_symmetry_xyhbond_nbd_refined0.138
r_symmetry_nbd_refined0.129
r_metal_ion_refined0.105
r_symmetry_xyhbond_nbd_other0.095
r_nbd_refined0.09
r_bond_other_d0.028
r_bond_refined_d0.023
r_gen_planes_refined0.019
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms509
Solvent Atoms112
Heterogen Atoms201

Software

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