1YC5

Sir2-p53 peptide-nicotinamide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.6293CHES, PEG3350, nicotinamide, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4850.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.1α = 90
b = 59.749β = 90
c = 106.121γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 42004-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A1.1NSLSX4A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.45099.40.0530.04626.16.8586735832122
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.41.45990.4140.3993.74.65707

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.4305859555273290399.430.18650.186260.18540.20218RANDOM16.796
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]
0.50.01-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.372
r_dihedral_angle_4_deg18.957
r_dihedral_angle_3_deg12.034
r_dihedral_angle_1_deg5.431
r_scangle_it3.748
r_scbond_it2.377
r_mcangle_it1.508
r_angle_refined_deg1.331
r_mcbond_it0.947
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.372
r_dihedral_angle_4_deg18.957
r_dihedral_angle_3_deg12.034
r_dihedral_angle_1_deg5.431
r_scangle_it3.748
r_scbond_it2.377
r_mcangle_it1.508
r_angle_refined_deg1.331
r_mcbond_it0.947
r_nbtor_refined0.31
r_nbd_refined0.203
r_symmetry_vdw_refined0.148
r_symmetry_hbond_refined0.133
r_xyhbond_nbd_refined0.107
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.008
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 Atoms1941
Nucleic Acid Atoms
Solvent Atoms266
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing