7KUK

High resolution 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 DROP4.62930.1 M Sodium acetate trihydrate pH 4.6, 2.0 M Sodium formate, 50 mM Magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
2.7855.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.391α = 90
b = 48.391β = 90
c = 82.304γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray99PIXELDECTRIS PILATUS3 6M2020-07-22MSINGLE 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
11.67501000.0380.0390.009191.2518.513505
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)
11.671.799.80.3280.3390.0830.996714.8

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 REPLACEMENTTHROUGHOUT5UEE1.67501186261687.9250.2030.20170.220917.097
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]
0.0080.0040.008-0.026
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it5.398
r_lrange_other5.189
r_angle_other_deg3.845
r_scangle_it3.675
r_scangle_other3.674
r_angle_refined_deg3.072
r_scbond_it2.397
r_scbond_other2.395
r_chiral_restr_other1.83
r_chiral_restr0.504
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it5.398
r_lrange_other5.189
r_angle_other_deg3.845
r_scangle_it3.675
r_scangle_other3.674
r_angle_refined_deg3.072
r_scbond_it2.397
r_scbond_other2.395
r_chiral_restr_other1.83
r_chiral_restr0.504
r_symmetry_xyhbond_nbd_refined0.261
r_nbtor_refined0.252
r_symmetry_nbtor_other0.239
r_xyhbond_nbd_refined0.232
r_symmetry_nbd_other0.216
r_nbd_other0.194
r_symmetry_nbd_refined0.119
r_nbd_refined0.104
r_bond_refined_d0.027
r_bond_other_d0.027
r_gen_planes_refined0.021
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms511
Solvent Atoms108
Heterogen Atoms195

Software

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