4BVB

CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND ADP-RIBOSE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4BV3PDB ENTRY 4BV3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.08 M KH2PO4 18 % PEG 8000 20% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.1242.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.5α = 90
b = 64.15β = 90
c = 67.83γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDCOLLIMATOR2011-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
1246.698.10.0718.6418341-3
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)
122.0593.10.373.93.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4BV3246.611742491798.080.173130.170050.23153RANDOM19.548
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]
0.23-0.470.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.131
r_dihedral_angle_4_deg17.664
r_dihedral_angle_3_deg15.222
r_dihedral_angle_1_deg6.137
r_mcangle_it2.583
r_scbond_it2.502
r_angle_refined_deg2.134
r_mcbond_it1.757
r_chiral_restr0.144
r_bond_refined_d0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.131
r_dihedral_angle_4_deg17.664
r_dihedral_angle_3_deg15.222
r_dihedral_angle_1_deg6.137
r_mcangle_it2.583
r_scbond_it2.502
r_angle_refined_deg2.134
r_mcbond_it1.757
r_chiral_restr0.144
r_bond_refined_d0.02
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2144
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing