7YUN

Crystal structure of human BEND6 BEN domain in complex with methylated DNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7YUK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2910.1 M carboxylic acids, 0.1 M imidazole, 0.1 M MES monohydrate (acid) (pH 6.5), 12.5% MPD (v/v), 12.5 % PEG 1000 (v/v), and 12.5% PEG 3350 (w/v).
Crystal Properties
Matthews coefficientSolvent content
2.2445.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.482α = 90
b = 67.276β = 100.72
c = 53.019γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON III2022-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1LIQUID ANODEBRUKER METALJET1.34138

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
12.1334.3499.90.055917.364.7715367
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)
12.132.1699.80.23984.53.14

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 REPLACEMENTTHROUGHOUT7YUK2.1334.341457178099.940.186940.184470.23356RANDOM24.344
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]
0.010.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.461
r_dihedral_angle_4_deg18.259
r_dihedral_angle_3_deg15.603
r_dihedral_angle_1_deg6.66
r_long_range_B_refined5.429
r_long_range_B_other5.337
r_scangle_other3.779
r_mcangle_it2.799
r_mcangle_other2.798
r_scbond_it2.437
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.461
r_dihedral_angle_4_deg18.259
r_dihedral_angle_3_deg15.603
r_dihedral_angle_1_deg6.66
r_long_range_B_refined5.429
r_long_range_B_other5.337
r_scangle_other3.779
r_mcangle_it2.799
r_mcangle_other2.798
r_scbond_it2.437
r_scbond_other2.437
r_mcbond_it1.854
r_mcbond_other1.851
r_angle_refined_deg1.647
r_angle_other_deg1.386
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.009
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 Atoms1465
Nucleic Acid Atoms488
Solvent Atoms155
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata scaling
SAINTdata reduction
PDB_EXTRACTdata extraction
PHASERphasing