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Tetramerization domain of zebrafish p53 (crystal form I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C26 PDB ENTRY 1C26
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: 50 MM ZINC ACETATE AND 20% (W/V) POLYETHYLENE GLYCOL 3,350.
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.853 α = 90 b = 120.611 β = 90 c = 61.029 γ = 90
Symmetry Space Group C 2 2 21
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 CCD 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 1.97 28.5 99.6 0.05 18.1 5.5 23226 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 1.97 2.08 99.3 0.65 2.8 5.5
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 PDB ENTRY 1C26 1.97 28.5 22029 1164 99.4 0.21876 0.21731 0.2265 0.24698 0.2367 RANDOM 55.187
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] 0.26 0.15 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.24 r_dihedral_angle_4_deg 16.93 r_dihedral_angle_3_deg 14.913 r_dihedral_angle_1_deg 4.641 r_scbond_it 3.016 r_mcangle_it 2.804 r_mcbond_it 2.043 r_mcbond_other 2.042 r_angle_refined_deg 1.342 r_angle_other_deg 0.764
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.24 r_dihedral_angle_4_deg 16.93 r_dihedral_angle_3_deg 14.913 r_dihedral_angle_1_deg 4.641 r_scbond_it 3.016 r_mcangle_it 2.804 r_mcbond_it 2.043 r_mcbond_other 2.042 r_angle_refined_deg 1.342 r_angle_other_deg 0.764 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 1939 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement