2ATA

Structural Basis of DNA Recognition by p53 Tetramers (complex II)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CA0PDB ENTRY 2CA0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.7293Lithium Chloride, PEG 3350, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3847.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.649α = 83.35
b = 57.998β = 87.55
c = 77.983γ = 73.5
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Osmic Inc. MSC - Blue Confocal Mirrors2004-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
12.243.0396.20.06819.193.8444444444431.4
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)
2.22.2593.593.50.2555.73.82862

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONISOMORPHOUS REPLACEMENTTHROUGHOUTPDB ENTRY 2CA02.2434444443333218897.50.1490.1490.1450.215RANDOM29.131
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]
-0.44-0.360.57-0.060.140.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.791
r_dihedral_angle_4_deg16.367
r_dihedral_angle_3_deg15.258
r_scangle_it7.454
r_dihedral_angle_1_deg7.266
r_scbond_it5.776
r_mcangle_it3.817
r_mcbond_it2.552
r_angle_refined_deg1.8
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.791
r_dihedral_angle_4_deg16.367
r_dihedral_angle_3_deg15.258
r_scangle_it7.454
r_dihedral_angle_1_deg7.266
r_scbond_it5.776
r_mcangle_it3.817
r_mcbond_it2.552
r_angle_refined_deg1.8
r_nbtor_refined0.312
r_symmetry_hbond_refined0.225
r_nbd_refined0.21
r_symmetry_vdw_refined0.194
r_xyhbond_nbd_refined0.17
r_chiral_restr0.107
r_metal_ion_refined0.102
r_bond_refined_d0.017
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6178
Nucleic Acid Atoms891
Solvent Atoms717
Heterogen Atoms4

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CNSphasing