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Sir2 H116A-deacetylated p53 peptide-3'-o-acetyl ADP ribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YC5 PDB Entry: 1yc5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 PEG 8000, Na-Tartrate:K-Phosphate, NaCl, NAD, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Crystal Properties Matthews coefficient Solvent content 2.4 48.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.996 α = 90 b = 46.996 β = 90 c = 257.081 γ = 90
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 4 2005-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.0 APS 24-ID-C
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 50 97.9 0.073 30.6 7.3 42845 42803 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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: 1yc5 1.9 50 2 42803 40570 2164 98.09 0.20714 0.20502 0.2266 0.24727 0.2319 RANDOM 34.511
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] 0.48 0.48 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.883 r_dihedral_angle_4_deg 18.145 r_dihedral_angle_3_deg 16.002 r_dihedral_angle_1_deg 6.342 r_scangle_it 4.419 r_scbond_it 2.835 r_angle_refined_deg 1.935 r_mcangle_it 1.86 r_mcbond_it 1.186 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.883 r_dihedral_angle_4_deg 18.145 r_dihedral_angle_3_deg 16.002 r_dihedral_angle_1_deg 6.342 r_scangle_it 4.419 r_scbond_it 2.835 r_angle_refined_deg 1.935 r_mcangle_it 1.86 r_mcbond_it 1.186 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.259 r_symmetry_hbond_refined 0.247 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.152 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 3952 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data scaling MOLREP phasing