2H59

Sir2 H116A-deacetylated p53 peptide-3'-o-acetyl ADP ribose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YC5PDB Entry: 1yc5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.2PEG 8000, Na-Tartrate:K-Phosphate, NaCl, NAD, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Crystal Properties
Matthews coefficientSolvent content
2.448.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.996α = 90
b = 46.996β = 90
c = 257.081γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C1.0APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.95097.90.07330.67.3428454280322

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB Entry: 1yc51.95024280340570216498.090.207140.205020.24727RANDOM34.511
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]
0.480.48-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.883
r_dihedral_angle_4_deg18.145
r_dihedral_angle_3_deg16.002
r_dihedral_angle_1_deg6.342
r_scangle_it4.419
r_scbond_it2.835
r_angle_refined_deg1.935
r_mcangle_it1.86
r_mcbond_it1.186
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.883
r_dihedral_angle_4_deg18.145
r_dihedral_angle_3_deg16.002
r_dihedral_angle_1_deg6.342
r_scangle_it4.419
r_scbond_it2.835
r_angle_refined_deg1.935
r_mcangle_it1.86
r_mcbond_it1.186
r_nbtor_refined0.315
r_symmetry_vdw_refined0.259
r_symmetry_hbond_refined0.247
r_nbd_refined0.234
r_xyhbond_nbd_refined0.164
r_chiral_restr0.152
r_bond_refined_d0.019
r_gen_planes_refined0.007
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 AtomsNumber
Protein Atoms3952
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-2000data scaling
MOLREPphasing