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Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs (p53-DNA complex 3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AC0 chain A of 2AC0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 293 0.20M AMMONIUM IODIDE, 20% PEG 3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 43.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.422 α = 90 b = 49.812 β = 93.48 c = 68.056 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r SILICON TOROIDAL MIRROR COATED WITH RHODIUM 2008-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97620 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.88 34.54 99.9 0.099 25.3 6.9 37958 -3 22.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.91 100 0.486 4.67 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT chain A of 2AC0 1.91 34.54 34235 1828 99.62 0.223 0.22059 0.2205 0.26642 0.2673 RANDOM 26.81
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 -0.45 0.5 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.386 r_dihedral_angle_3_deg 14.782 r_dihedral_angle_4_deg 13.662 r_dihedral_angle_1_deg 7.467 r_scangle_it 6.507 r_scbond_it 4.925 r_mcangle_it 3.89 r_angle_refined_deg 2.819 r_mcbond_it 2.447 r_chiral_restr 0.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.386 r_dihedral_angle_3_deg 14.782 r_dihedral_angle_4_deg 13.662 r_dihedral_angle_1_deg 7.467 r_scangle_it 6.507 r_scbond_it 4.925 r_mcangle_it 3.89 r_angle_refined_deg 2.819 r_mcbond_it 2.447 r_chiral_restr 0.192 r_bond_refined_d 0.031 r_gen_planes_refined 0.016 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 Atoms Number Protein Atoms 2972 Nucleic Acid Atoms 410 Solvent Atoms 311 Heterogen Atoms 4
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling