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Structural Basis of DNA Recognition by p53 Tetramers (complex I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TSR PDB ENTRY 1TSR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 293 Ammonium Formate, PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 44.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.439 α = 82.93 b = 58.146 β = 87.99 c = 77.539 γ = 73.6
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 2004-09-04 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 1.8 40 94.2 0.055 24.5 4 79253 79253 28.6
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) 1.8 1.83 90.6 90.6 0.342 4 3.8 3842
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1TSR 1.8 33.52 79253 77487 3896 97.78 0.157 0.157 0.153 0.1598 0.217 0.1578 RANDOM 28.16
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 -0.05 0.53 -0.67 0.05 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.708 r_dihedral_angle_4_deg 16.777 r_dihedral_angle_3_deg 14.216 r_dihedral_angle_1_deg 6.636 r_scangle_it 6.206 r_scbond_it 4.535 r_mcangle_it 3.496 r_mcbond_it 2.508 r_angle_refined_deg 1.754 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.708 r_dihedral_angle_4_deg 16.777 r_dihedral_angle_3_deg 14.216 r_dihedral_angle_1_deg 6.636 r_scangle_it 6.206 r_scbond_it 4.535 r_mcangle_it 3.496 r_mcbond_it 2.508 r_angle_refined_deg 1.754 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.248 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.187 r_metal_ion_refined 0.126 r_chiral_restr 0.119 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6217 Nucleic Acid Atoms 972 Solvent Atoms 1054 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CNS phasing