7RBF

Human DNA polymerase beta crosslinked binary complex - B


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52980.1 M Citrate pH 5.5, 18% PEG6000
Crystal Properties
Matthews coefficientSolvent content
2.4649.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.68α = 90
b = 79.571β = 91.68
c = 54.828γ = 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
11.8445.1398.90.0480.0560.0290.99912.63.840114
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)
11.841.8897.80.4010.4750.250.873.5

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 REPLACEMENTTHROUGHOUT1BPX1.8445.1338054204798.750.17760.17590.2083RANDOM26.104
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]
0.830.210.13-0.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.898
r_dihedral_angle_3_deg15.553
r_dihedral_angle_4_deg15.247
r_dihedral_angle_1_deg5.83
r_angle_refined_deg1.725
r_angle_other_deg1.462
r_chiral_restr0.122
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.898
r_dihedral_angle_3_deg15.553
r_dihedral_angle_4_deg15.247
r_dihedral_angle_1_deg5.83
r_angle_refined_deg1.725
r_angle_other_deg1.462
r_chiral_restr0.122
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2561
Nucleic Acid Atoms628
Solvent Atoms384
Heterogen Atoms45

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing