4C7B

Complex of human Sirt3 with Bromo-Resveratrol and Fluor-De-Lys peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4H8DPDB ENTRY 4H8D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17200 MM NACL,100 MM HEPES PH 7, 10% (V/V) ISOPROPANOL
Crystal Properties
Matthews coefficientSolvent content
2.5151

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.82α = 90
b = 114.82β = 90
c = 123.75γ = 120
Symmetry
Space GroupH 3 2

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
12.146.199.90.0814.33.935487-3
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)
12.12.299.90.722.13.9

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 4H8D2.146.131758592599.970.183050.180460.23402RANDOM39.286
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]
-0.71-0.35-0.712.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.827
r_dihedral_angle_4_deg18.029
r_dihedral_angle_3_deg14.646
r_long_range_B_refined9.015
r_long_range_B_other9.014
r_dihedral_angle_1_deg6.674
r_scangle_other3.588
r_mcangle_it2.81
r_mcangle_other2.809
r_scbond_it2.382
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.827
r_dihedral_angle_4_deg18.029
r_dihedral_angle_3_deg14.646
r_long_range_B_refined9.015
r_long_range_B_other9.014
r_dihedral_angle_1_deg6.674
r_scangle_other3.588
r_mcangle_it2.81
r_mcangle_other2.809
r_scbond_it2.382
r_scbond_other2.381
r_angle_refined_deg2.118
r_mcbond_it1.715
r_mcbond_other1.715
r_angle_other_deg1.069
r_chiral_restr0.113
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.003
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 Atoms2113
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing