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Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs (p53-DNA complex 1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 293 0.16M SODIUM ACETATE, 16% PEG 3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.161 α = 90 b = 49.841 β = 93.96 c = 33.962 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 IMAGE PLATE RIGAKU RAXIS IV++ OSMIC INC. MSC-BLUE CONFOCAL MIRRORS 2005-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 1.8 29 95 0.049 32.1 5.1 20255 27.68
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 1.8 1.83 91.6 0.225 6.3 5 974
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 3IGK 1.8 24.92 19216 1037 95 0.15093 0.14765 0.146 0.21195 0.2029 RANDOM 28.753
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] -0.9 -0.6 0.3 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.025 r_dihedral_angle_4_deg 16.153 r_dihedral_angle_3_deg 12.294 r_scangle_it 7.231 r_dihedral_angle_1_deg 6.815 r_scbond_it 5.525 r_mcangle_it 4.089 r_mcbond_it 2.767 r_angle_refined_deg 2.347 r_chiral_restr 0.174
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.025 r_dihedral_angle_4_deg 16.153 r_dihedral_angle_3_deg 12.294 r_scangle_it 7.231 r_dihedral_angle_1_deg 6.815 r_scbond_it 5.525 r_mcangle_it 4.089 r_mcbond_it 2.767 r_angle_refined_deg 2.347 r_chiral_restr 0.174 r_bond_refined_d 0.026 r_gen_planes_refined 0.014 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 1539 Nucleic Acid Atoms 225 Solvent Atoms 340 Heterogen Atoms 5
Software Software Software Name Purpose HKL-2000 data collection CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing