3KZ8

Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs (p53-DNA complex 3)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AC0chain A of 2AC0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.12930.20M AMMONIUM IODIDE, 20% PEG 3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.243.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.422α = 90
b = 49.812β = 93.48
c = 68.056γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rSILICON TOROIDAL MIRROR COATED WITH RHODIUM2008-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97620ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.8834.5499.90.09925.36.937958-322.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.911000.4864.677.2

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 REPLACEMENTTHROUGHOUTchain A of 2AC01.9134.5434235182899.620.2230.220590.26642RANDOM26.81
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]
-0.71-0.450.50.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.386
r_dihedral_angle_3_deg14.782
r_dihedral_angle_4_deg13.662
r_dihedral_angle_1_deg7.467
r_scangle_it6.507
r_scbond_it4.925
r_mcangle_it3.89
r_angle_refined_deg2.819
r_mcbond_it2.447
r_chiral_restr0.192
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.386
r_dihedral_angle_3_deg14.782
r_dihedral_angle_4_deg13.662
r_dihedral_angle_1_deg7.467
r_scangle_it6.507
r_scbond_it4.925
r_mcangle_it3.89
r_angle_refined_deg2.819
r_mcbond_it2.447
r_chiral_restr0.192
r_bond_refined_d0.031
r_gen_planes_refined0.016
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2972
Nucleic Acid Atoms410
Solvent Atoms311
Heterogen Atoms4

Software

Software
Software NamePurpose
DNAdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling