5D7Q

Crystal structure of human Sirt2 in complex with ADPR and CHIC35


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5D7O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.7529318 % (w/v) PEG 10000, 0.1 M Bis-Tris
Crystal Properties
Matthews coefficientSolvent content
2.5251.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.34α = 90
b = 78.17β = 90
c = 114.68γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2013-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.0146.2399.60.1097.6446758
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.012.060.716

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5D7O2.0146.2344359234999.40.211660.210970.22459RANDOM34.278
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]
0.940.06-1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.5
r_dihedral_angle_3_deg14.166
r_dihedral_angle_4_deg13.832
r_dihedral_angle_1_deg6.014
r_long_range_B_refined4.046
r_long_range_B_other4.03
r_scangle_other2.371
r_mcangle_other2.143
r_mcangle_it2.142
r_scbond_it1.412
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.5
r_dihedral_angle_3_deg14.166
r_dihedral_angle_4_deg13.832
r_dihedral_angle_1_deg6.014
r_long_range_B_refined4.046
r_long_range_B_other4.03
r_scangle_other2.371
r_mcangle_other2.143
r_mcangle_it2.142
r_scbond_it1.412
r_scbond_other1.409
r_mcbond_it1.311
r_mcbond_other1.311
r_angle_refined_deg1.308
r_angle_other_deg0.784
r_chiral_restr0.069
r_bond_refined_d0.007
r_bond_other_d0.006
r_gen_planes_refined0.004
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4775
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms146

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing