5WM1

Structure of the 10S (+)-trans-BP-dG modified Rev1 ternary complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AQ4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62930.25 M sodium citrate pH 6.0 buffer 15-20% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.3347.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.002α = 90
b = 64.879β = 90
c = 130.652γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.1NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.854599.726.37.247446

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 REPLACEMENTTHROUGHOUT2AQ41.8565.3344991238999.50.171950.170120.20649RANDOM25.19
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]
-1.051.010.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.254
r_dihedral_angle_4_deg16.777
r_dihedral_angle_3_deg12.502
r_dihedral_angle_1_deg5.691
r_long_range_B_refined5.011
r_long_range_B_other4.857
r_scangle_other3.101
r_mcangle_it2.276
r_mcangle_other2.276
r_scbond_it1.959
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.254
r_dihedral_angle_4_deg16.777
r_dihedral_angle_3_deg12.502
r_dihedral_angle_1_deg5.691
r_long_range_B_refined5.011
r_long_range_B_other4.857
r_scangle_other3.101
r_mcangle_it2.276
r_mcangle_other2.276
r_scbond_it1.959
r_scbond_other1.956
r_mcbond_it1.421
r_mcbond_other1.421
r_angle_refined_deg1.383
r_angle_other_deg1
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms3443
Nucleic Acid Atoms571
Solvent Atoms335
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing