6QIB

The crystal structure of Pol2CORE in complex with DNA and an incoming nucleotide, carrying an Fe-S cluster


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4M8O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829110mM Tris HCl pH8, 10mM CaCl2, 15% PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.8757.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 158.36α = 90
b = 70.402β = 112.99
c = 154.24γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2018-09-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.96770ESRFMASSIF-3

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
12.878.4898.50.1260.1430.0660.9957.84.338251
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)
12.82.9299.21.0821.2240.5610.4474.5

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 REPLACEMENTTHROUGHOUT4m8o2.878.4836257186898.350.22650.22340.2856RANDOM69.068
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]
18.51-6.7824.36-42.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.985
r_dihedral_angle_3_deg19.209
r_dihedral_angle_4_deg17.039
r_dihedral_angle_1_deg7.009
r_angle_refined_deg1.057
r_chiral_restr0.096
r_gen_planes_refined0.004
r_bond_refined_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8608
Nucleic Acid Atoms529
Solvent Atoms
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
Cootmodel building
PHASERphasing