5U2R

PRECATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED DNA SUBSTARTE, INCOMING L-DCTP AND CA2+


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829550 MM IMIDAZOLE, 350 MM SODIUM ACETATE, 17% PEG3350,
Crystal Properties
Matthews coefficientSolvent content
2.2244.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.91α = 90
b = 80.16β = 107.68
c = 55.64γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray193CCDRAYONIX MX225HE2013-10-11MSINGLE 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)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
11.826.9699.80.1128.95.439460
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.841000.6322.55.3

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 REPLACEMENTTHROUGHOUT4RPX1.826.9637460197899.80.1920.1910.229RANDOM20.28
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]
0.06-0.040.1-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.888
r_dihedral_angle_4_deg16.484
r_dihedral_angle_3_deg13.889
r_dihedral_angle_1_deg4.916
r_long_range_B_refined3.946
r_long_range_B_other3.78
r_scangle_other2.13
r_mcangle_it1.699
r_mcangle_other1.698
r_scbond_it1.293
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.888
r_dihedral_angle_4_deg16.484
r_dihedral_angle_3_deg13.889
r_dihedral_angle_1_deg4.916
r_long_range_B_refined3.946
r_long_range_B_other3.78
r_scangle_other2.13
r_mcangle_it1.699
r_mcangle_other1.698
r_scbond_it1.293
r_scbond_other1.293
r_angle_refined_deg1.148
r_mcbond_it0.99
r_mcbond_other0.986
r_angle_other_deg0.839
r_chiral_restr0.065
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2633
Nucleic Acid Atoms632
Solvent Atoms286
Heterogen Atoms44

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement