2XSD

Crystal Structure of the dimeric Oct-6 (Pou3f1) POU domain bound to palindromic MORE DNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E3OPDB ENTRY 1E3O

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.6RESERVOIR: 0.2M MGCL2, 14%PEG4000 AND 0.1 SODIUM CITRATE PH5.6 PROTEIN-DNA COMPLEX: 10MG/ML IN 10 MM HEPES PH 7.0; 100 MM NACL EUQAL RESERVOIR AND PROTEIN VOLUMES MIXED
Crystal Properties
Matthews coefficientSolvent content
2.6959.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.497α = 90
b = 52.009β = 129.03
c = 69.013γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2010-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
12.055098.10.0431.77.2159652
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)
12.052.1289.20.451.95.1

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 1E3O2.04941.3891.3415949159997.630.19780.1940.231772.2
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]
-0.70218.07455.6341-4.9321
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d21.582
f_angle_d1.153
f_chiral_restr0.057
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1025
Nucleic Acid Atoms431
Solvent Atoms38
Heterogen Atoms16

Software

Software
Software NamePurpose
PHENIXrefinement
PHASERphasing