7RBE

Human DNA polymerase beta crosslinked binary complex - A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52940.1 M Citrate pH 5.5, 18% PEG6000
Crystal Properties
Matthews coefficientSolvent content
2.3748.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.585α = 90
b = 79.48β = 104.55
c = 54.906γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2016-02-17MSINGLE 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
11.8944.1896.80.0580.0680.0350.99810.43.734956
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)
11.891.9478.50.5170.6220.3390.7192.9

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 REPLACEMENTTHROUGHOUT1BPX1.8944.1833220172596.660.21880.21640.2677RANDOM28.592
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]
0.680.030.72-1.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.518
r_dihedral_angle_3_deg17.139
r_dihedral_angle_4_deg15.699
r_dihedral_angle_1_deg6.078
r_angle_refined_deg1.602
r_angle_other_deg1.392
r_chiral_restr0.104
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.518
r_dihedral_angle_3_deg17.139
r_dihedral_angle_4_deg15.699
r_dihedral_angle_1_deg6.078
r_angle_refined_deg1.602
r_angle_other_deg1.392
r_chiral_restr0.104
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2510
Nucleic Acid Atoms628
Solvent Atoms443
Heterogen Atoms54

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing