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Human p53 core domain with hot spot mutation R249S and second-site suppressor mutations H168R and T123A
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 6.1 293 0.2M Sodium Acetate, 20% PEG 3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.518 α = 90 b = 45.518 β = 90 c = 327.424 γ = 120
Symmetry Space Group P 65 2 2
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 QUANTUM 210 Sagitally focusing Ge(220) and a multilayer 2007-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.93400 ESRF ID14-1
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 1.9 44 98.8 0.069 33.5 9.9 17068 17068 23.4
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) 1.9 1.93 90.4 0.292 4.5 5.4 729
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 1.9 37.09 16072 16072 859 98.8 0.2068 0.20678 0.20387 0.2101 0.26209 0.2662 RANDOM 23.366
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] -0.01 -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.39 r_dihedral_angle_3_deg 12.769 r_dihedral_angle_4_deg 11.764 r_scangle_it 8.326 r_scbond_it 6.761 r_dihedral_angle_1_deg 6.389 r_mcangle_it 5.081 r_mcbond_it 3.844 r_angle_refined_deg 1.422 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.39 r_dihedral_angle_3_deg 12.769 r_dihedral_angle_4_deg 11.764 r_scangle_it 8.326 r_scbond_it 6.761 r_dihedral_angle_1_deg 6.389 r_mcangle_it 5.081 r_mcbond_it 3.844 r_angle_refined_deg 1.422 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.23 r_symmetry_hbond_refined 0.207 r_xyhbond_nbd_refined 0.202 r_nbd_refined 0.2 r_metal_ion_refined 0.129 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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 1517 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing