7R3X

The crystal structure of the L439V variant of Pol2CORE in complex with DNA and an incoming nucleotide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52928 % PEG 20K , 150 mM NaAc, 0-1,5% Glycerol, 50 mM MES pH6.5
Crystal Properties
Matthews coefficientSolvent content
2.8757.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 221.505α = 90
b = 70.685β = 100.14
c = 111.639γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2020-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.976254MAX IVBioMAX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
12.4645.7899.80.9440.9977.954.256190656.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.462.6599.90.9440.5960.974.25

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 REPLACEMENTTHROUGHOUT4m8o2.4645.7858947307099.830.21190.20950.2562RANDOM73.254
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]
-2.310.231.131.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.502
r_dihedral_angle_4_deg21.528
r_dihedral_angle_3_deg18.397
r_dihedral_angle_1_deg6.993
r_angle_refined_deg1.672
r_angle_other_deg1.297
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.502
r_dihedral_angle_4_deg21.528
r_dihedral_angle_3_deg18.397
r_dihedral_angle_1_deg6.993
r_angle_refined_deg1.672
r_angle_other_deg1.297
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9036
Nucleic Acid Atoms529
Solvent Atoms96
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing