6S9T

Dimerization domain of Xenopus laevis LDB1 in complex with darpin 3


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1 M TrisHCL, pH 7.0 32% PEG200 0.05 M Li2SO4
Crystal Properties
Matthew coefficientSolvent content
2.5551.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.217α = 90
b = 70.217β = 90
c = 122.257γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2017-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.978860DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.0543.1599.920.1270.1290.021123.539.522528
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.12

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.0543.1521557107199.910.22060.21790.2793RANDOM57.123
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]
-0.84-0.42-0.842.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.184
r_dihedral_angle_4_deg24.469
r_dihedral_angle_3_deg16.869
r_dihedral_angle_1_deg6.531
r_angle_refined_deg1.722
r_angle_other_deg1.304
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.184
r_dihedral_angle_4_deg24.469
r_dihedral_angle_3_deg16.869
r_dihedral_angle_1_deg6.531
r_angle_refined_deg1.722
r_angle_other_deg1.304
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2369
Nucleic Acid Atoms
Solvent Atoms27
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
SHELXCDphasing
XDSdata reduction