5WMB

Structure of the 10S (-)-cis-BP-dG modified Rev1 ternary complex (the BP residue is disordered)


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
2.3447.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.307α = 90
b = 65.476β = 90
c = 131.657γ = 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 X251.10NSLSX25

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
12.2565.8310018.67.426824

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 REPLACEMENTTHROUGHOUT2AQ42.2565.8325424134599.820.172230.16990.2171RANDOM38.837
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]
-1.31.91-0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.036
r_dihedral_angle_4_deg16.709
r_dihedral_angle_3_deg15.223
r_long_range_B_refined7.421
r_long_range_B_other7.404
r_dihedral_angle_1_deg5.861
r_scangle_other5.243
r_mcangle_other3.534
r_mcangle_it3.533
r_scbond_it3.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.036
r_dihedral_angle_4_deg16.709
r_dihedral_angle_3_deg15.223
r_long_range_B_refined7.421
r_long_range_B_other7.404
r_dihedral_angle_1_deg5.861
r_scangle_other5.243
r_mcangle_other3.534
r_mcangle_it3.533
r_scbond_it3.295
r_scbond_other3.28
r_mcbond_it2.26
r_mcbond_other2.257
r_angle_refined_deg1.474
r_angle_other_deg1.011
r_chiral_restr0.086
r_bond_refined_d0.011
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 Atoms3436
Nucleic Acid Atoms552
Solvent Atoms161
Heterogen Atoms91

Software

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