5WM8

Structure of the 10R (+)-cis-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
2.6453.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.551α = 90
b = 180.358β = 90
c = 54.586γ = 90
Symmetry
Space GroupP 21 21 2

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 X251.100NSLSX25

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
11.925095.320.25.845446

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 REPLACEMENTTHROUGHOUT2AQ41.924543093229094.990.178270.176330.21359RANDOM32.109
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]
-0.45-0.250.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.342
r_dihedral_angle_4_deg17.164
r_dihedral_angle_3_deg13.654
r_dihedral_angle_1_deg5.772
r_long_range_B_refined5.409
r_long_range_B_other5.252
r_scangle_other3.512
r_mcangle_it2.71
r_mcangle_other2.71
r_scbond_it2.196
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.342
r_dihedral_angle_4_deg17.164
r_dihedral_angle_3_deg13.654
r_dihedral_angle_1_deg5.772
r_long_range_B_refined5.409
r_long_range_B_other5.252
r_scangle_other3.512
r_mcangle_it2.71
r_mcangle_other2.71
r_scbond_it2.196
r_scbond_other2.195
r_mcbond_it1.728
r_mcbond_other1.727
r_angle_refined_deg1.394
r_angle_other_deg0.988
r_chiral_restr0.075
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms3434
Nucleic Acid Atoms571
Solvent Atoms311
Heterogen Atoms123

Software

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