2AC0

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TSRPDB ENTRY 1TSR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.6293Ammonium Formate, PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.344.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.439α = 82.93
b = 58.146β = 87.99
c = 77.539γ = 73.6
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 Mirrors2004-09-04MSINGLE 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
11.84094.20.05524.54792537925328.6
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)
1.81.8390.690.60.34243.83842

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1TSR1.833.527925377487389697.780.1570.1570.1530.217RANDOM28.16
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]
-0.11-0.050.53-0.670.050.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.708
r_dihedral_angle_4_deg16.777
r_dihedral_angle_3_deg14.216
r_dihedral_angle_1_deg6.636
r_scangle_it6.206
r_scbond_it4.535
r_mcangle_it3.496
r_mcbond_it2.508
r_angle_refined_deg1.754
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.708
r_dihedral_angle_4_deg16.777
r_dihedral_angle_3_deg14.216
r_dihedral_angle_1_deg6.636
r_scangle_it6.206
r_scbond_it4.535
r_mcangle_it3.496
r_mcbond_it2.508
r_angle_refined_deg1.754
r_nbtor_refined0.311
r_symmetry_hbond_refined0.248
r_nbd_refined0.207
r_symmetry_vdw_refined0.198
r_xyhbond_nbd_refined0.187
r_metal_ion_refined0.126
r_chiral_restr0.119
r_bond_refined_d0.016
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6217
Nucleic Acid Atoms972
Solvent Atoms1054
Heterogen Atoms4

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CNSphasing