6VG8

Crystal structure of the DNA binding domains of human FLI1 and Runx2 in complex with 16-mer DNA CAGAGGATGTGGCTTC


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5JVT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2947% w/v PEG 4000, 50 mM Na Citrate, pH 5.6, 4% v/v isopropanol
Crystal Properties
Matthews coefficientSolvent content
7.2282.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.427α = 90
b = 104.427β = 90
c = 326.382γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2016-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-ID

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
13.255093.80.13112.97.916635
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)
13.253.310.433

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 REPLACEMENTTHROUGHOUT5JVT4.3134.21729840999.250.27360.2730.2827RANDOM246.997
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]
6.153.086.15-19.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.043
r_dihedral_angle_3_deg17.33
r_dihedral_angle_4_deg11.565
r_dihedral_angle_1_deg7.928
r_angle_refined_deg1.221
r_angle_other_deg1.177
r_chiral_restr0.053
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.043
r_dihedral_angle_3_deg17.33
r_dihedral_angle_4_deg11.565
r_dihedral_angle_1_deg7.928
r_angle_refined_deg1.221
r_angle_other_deg1.177
r_chiral_restr0.053
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1720
Nucleic Acid Atoms656
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing