X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AFKAFK1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5291PROTEIN WAS CRYSTALLIZED FROM 25%, PEG 3350, 20 MM SODIUM CITRATE, PH 5.5, Glycinyl-O5'-adenosine phosphoramidate was soaked into the crystals using a stock solution of 100 mM, to achieve ~35 mM in the soaking solution
Crystal Properties
Matthews coefficientSolvent content
2.1843.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.756α = 90
b = 32.686β = 90.46
c = 72.723γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2019-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.65099.40.0550.060.02410.25.831715
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)
11.61.6698.90.7750.8580.3630.685.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTAFK11.641.630209150698.980.18620.18370.2374RANDOM29.636
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]
0.050.28-0.02-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.949
r_dihedral_angle_3_deg12.228
r_dihedral_angle_4_deg10.227
r_dihedral_angle_1_deg6.501
r_angle_other_deg1.358
r_angle_refined_deg1.345
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.949
r_dihedral_angle_3_deg12.228
r_dihedral_angle_4_deg10.227
r_dihedral_angle_1_deg6.501
r_angle_other_deg1.358
r_angle_refined_deg1.345
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1902
Nucleic Acid Atoms
Solvent Atoms199
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
MOLREPphasing