5D7P

Crystal structure of human Sirt2 in complex with ADPR and EX-243


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
2.4650.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.496α = 90
b = 77.578β = 90
c = 114.206γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2013-07-12MSINGLE 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
11.7639.4197.80.0818.914.366454
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)
11.761.791.136

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 REPLACEMENTTHROUGHOUT5D7O1.7639.4163026336797.590.191820.19010.22444RANDOM34.863
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]
1.62-0.44-1.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.387
r_dihedral_angle_4_deg14.582
r_dihedral_angle_3_deg13.136
r_dihedral_angle_1_deg5.706
r_long_range_B_refined4.53
r_long_range_B_other4.465
r_scangle_other2.55
r_mcangle_it2.103
r_mcangle_other2.103
r_scbond_it1.514
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.387
r_dihedral_angle_4_deg14.582
r_dihedral_angle_3_deg13.136
r_dihedral_angle_1_deg5.706
r_long_range_B_refined4.53
r_long_range_B_other4.465
r_scangle_other2.55
r_mcangle_it2.103
r_mcangle_other2.103
r_scbond_it1.514
r_scbond_other1.514
r_angle_refined_deg1.34
r_mcbond_it1.296
r_mcbond_other1.295
r_angle_other_deg0.791
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
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 Atoms289
Heterogen Atoms149

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing