☰ Navigation Tabs
Structural Basis of DNA Recognition by p53 Tetramers (complex II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CA0 PDB ENTRY 2CA0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 293 Lithium Chloride, PEG 3350, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.38 47.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.649 α = 83.35 b = 57.998 β = 87.55 c = 77.983 γ = 73.5
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 2004-09-16 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 Merge 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 2.2 43.03 96.2 0.068 19.19 3.8 44444 44444 31.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.25 93.5 93.5 0.255 5.7 3.8 2862
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 ISOMORPHOUS REPLACEMENT THROUGHOUT PDB ENTRY 2CA0 2.2 43 44444 43333 2188 97.5 0.149 0.149 0.145 0.1489 0.215 0.2187 RANDOM 29.131
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 -0.36 0.57 -0.06 0.14 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.791 r_dihedral_angle_4_deg 16.367 r_dihedral_angle_3_deg 15.258 r_scangle_it 7.454 r_dihedral_angle_1_deg 7.266 r_scbond_it 5.776 r_mcangle_it 3.817 r_mcbond_it 2.552 r_angle_refined_deg 1.8 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.791 r_dihedral_angle_4_deg 16.367 r_dihedral_angle_3_deg 15.258 r_scangle_it 7.454 r_dihedral_angle_1_deg 7.266 r_scbond_it 5.776 r_mcangle_it 3.817 r_mcbond_it 2.552 r_angle_refined_deg 1.8 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.225 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.107 r_metal_ion_refined 0.102 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6178 Nucleic Acid Atoms 891 Solvent Atoms 717 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CNS phasing