7RBK

Human DNA polymerase beta crosslinked complex, 40 s Ca to Mg exchange


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52980.1 M Citrate pH 5.5, 18% PEG6000
Crystal Properties
Matthews coefficientSolvent content
2.244.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.558α = 90
b = 80.398β = 107.64
c = 55.419γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2019-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97931APS31-ID

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
12.248.1898.50.0850.0920.0350.99815.46.821335
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)
12.22.2699.10.4930.5370.210.9196.4

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 REPLACEMENTTHROUGHOUT4RPY2.248.1820277103498.260.20040.19770.2513RANDOM31.515
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]
2.260.32-0.21-1.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.978
r_dihedral_angle_3_deg14.311
r_dihedral_angle_4_deg13.396
r_dihedral_angle_1_deg5.549
r_angle_other_deg1.161
r_angle_refined_deg1.11
r_chiral_restr0.049
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.978
r_dihedral_angle_3_deg14.311
r_dihedral_angle_4_deg13.396
r_dihedral_angle_1_deg5.549
r_angle_other_deg1.161
r_angle_refined_deg1.11
r_chiral_restr0.049
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2539
Nucleic Acid Atoms650
Solvent Atoms116
Heterogen Atoms94

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing