2H4J

Sir2-deacetylated peptide (from enzymatic turnover in crystal)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.6293CHES, PEG3350, PH9.6, acetylated peptide. Crystals were soaked in cryo + 5mM NAD, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4950.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.049α = 90
b = 59.683β = 90
c = 107.35γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-CAPS14-BM-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
12.15099.90.09220.36.9179331697322

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: 1yc52.1502168861697391399.940.199990.197620.24619RANDOM30.982
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]
0.390.08-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.645
r_dihedral_angle_4_deg19.404
r_dihedral_angle_3_deg13.714
r_sphericity_free7.971
r_dihedral_angle_1_deg6.467
r_scangle_it4.765
r_rigid_bond_restr4.503
r_scbond_it4.39
r_sphericity_bonded3.349
r_mcangle_it2.394
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.645
r_dihedral_angle_4_deg19.404
r_dihedral_angle_3_deg13.714
r_sphericity_free7.971
r_dihedral_angle_1_deg6.467
r_scangle_it4.765
r_rigid_bond_restr4.503
r_scbond_it4.39
r_sphericity_bonded3.349
r_mcangle_it2.394
r_angle_refined_deg1.744
r_mcbond_it1.612
r_nbtor_refined0.302
r_nbd_refined0.227
r_symmetry_hbond_refined0.16
r_symmetry_vdw_refined0.158
r_xyhbond_nbd_refined0.137
r_chiral_restr0.11
r_bond_refined_d0.019
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1936
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data scaling
CNSphasing