3US0

Structure of p63 DNA Binding Domain in Complex with a 22 Base Pair A/T Rich Response Element Containing a Two Base Pair "AT" Spacer Between Half Sites


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QYNPDB ENTRY 3QYN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829814% PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.3363.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.806α = 90
b = 141.806β = 90
c = 119.604γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrors2010-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.03320357APS23-ID-D

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
12.56099.990.08219.912.847269472581.53.550.4
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)
12.52.561000.4513.59.63446

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3QYN2.559.8021.54726947224242499.910.20770.2060.2389RANDOM
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]
8.46198.4619-16.9237
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d20.344
f_angle_d1.643
f_chiral_restr0.102
f_bond_d0.011
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5985
Nucleic Acid Atoms896
Solvent Atoms394
Heterogen Atoms4

Software

Software
Software NamePurpose
JBluIce-EPICSdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling