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Tetramerization domain of zebrafish p53 (crystal form II)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 SITTING DROP VAPOR DIFFUSION AT 20 DEGREE C; PROTEIN SOLUTION: 12 MG/ML IN 20 MM TRIS PH 7.5, 50 MM NACL, 5 MM DTT; CRYSTALLIZATION BUFFER: 160 MM ZINC ACETATE, 80 MM SODIUM CACODYLATE, PH 6.5, 12% (W/V) POLYETHYLENE GLYCOL 8,000 AND 19% (W/V) GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.6 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.861 α = 90 b = 74.507 β = 117.79 c = 74.945 γ = 90
Symmetry Space Group P 1 21 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 28.9 99.3 0.04 14.8 3.4 34925 2
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 2.2 2.32 99.5 0.52 2.5 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.2 28.9 33164 1744 99.24 0.22845 0.2259 0.234 0.27996 0.2279 RANDOM 57.722
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] 2.2 -0.29 -0.14 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.097 r_dihedral_angle_4_deg 19.387 r_dihedral_angle_3_deg 17.22 r_dihedral_angle_1_deg 4.824 r_mcangle_it 2.369 r_scbond_it 2.057 r_mcbond_it 1.626 r_mcbond_other 1.625 r_angle_refined_deg 1.336 r_angle_other_deg 0.777
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.097 r_dihedral_angle_4_deg 19.387 r_dihedral_angle_3_deg 17.22 r_dihedral_angle_1_deg 4.824 r_mcangle_it 2.369 r_scbond_it 2.057 r_mcbond_it 1.626 r_mcbond_other 1.625 r_angle_refined_deg 1.336 r_angle_other_deg 0.777 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3964 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement