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Human p53 core domain with hot spot mutation R249S (III)
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 2.17 43.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.224 α = 90 b = 68.477 β = 101.34 c = 57.832 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 IMAGE PLATE RIGAKU RAXIS IV++ Osmic Inc. MSC-Blue confocal mirrors 2004-07-21 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 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 2.2 37 100 0.133 13.1 5.65 19630 19630
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) 2.2 2.24 100 0.415 4.5 5.1 972
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 2.2 34.24 18609 18609 1003 99.79 0.1678 0.16778 0.16311 0.1627 0.25627 0.2579 RANDOM 13.974
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.49 r_dihedral_angle_4_deg 22.622 r_dihedral_angle_3_deg 18.086 r_scangle_it 7.486 r_dihedral_angle_1_deg 7.098 r_scbond_it 5.978 r_mcangle_it 3.715 r_mcbond_it 2.481 r_angle_refined_deg 1.912 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.49 r_dihedral_angle_4_deg 22.622 r_dihedral_angle_3_deg 18.086 r_scangle_it 7.486 r_dihedral_angle_1_deg 7.098 r_scbond_it 5.978 r_mcangle_it 3.715 r_mcbond_it 2.481 r_angle_refined_deg 1.912 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.262 r_symmetry_hbond_refined 0.23 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.126 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 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_refined 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 3055 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing