7YUL

Crystal structure of human BEND6 BEN domain in complex with DNA


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2910.12 M Ethylene glycol, 0.1 M Sodium HEPES, 0.1 M MOPS (acid), 12.5% MPD (v/v), 12.5% PEG 1000 (v/v), 12.5% PEG3350 (v/v)
Crystal Properties
Matthews coefficientSolvent content
1.9436.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.092α = 90
b = 39.514β = 90
c = 43.719γ = 90
Symmetry
Space GroupP 21 21 2

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
11.8227.1199.40.045134.157.6911195
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)
11.821.8592.70.1599.773.26

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 REPLACEMENTTHROUGHOUT7YUG1.8227.111059956799.370.15940.15750.1943RANDOM16.862
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]
-0.040.020.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.544
r_dihedral_angle_4_deg15.154
r_dihedral_angle_3_deg13.785
r_dihedral_angle_1_deg6.303
r_angle_refined_deg1.826
r_angle_other_deg1.488
r_chiral_restr0.098
r_gen_planes_refined0.013
r_bond_refined_d0.011
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.544
r_dihedral_angle_4_deg15.154
r_dihedral_angle_3_deg13.785
r_dihedral_angle_1_deg6.303
r_angle_refined_deg1.826
r_angle_other_deg1.488
r_chiral_restr0.098
r_gen_planes_refined0.013
r_bond_refined_d0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms737
Nucleic Acid Atoms243
Solvent Atoms140
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SAINTdata scaling
PDB_EXTRACTdata extraction
PHASERphasing