6ACE

histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RIY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52950.1M sodium cacodylate (pH 5.5), 25%(w/v) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.3547.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.227α = 90
b = 41.169β = 94.69
c = 55.854γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.9793SSRFBL19U1

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
11.9861.4192.60.107114.518297
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)
11.982.010.516

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 REPLACEMENTTHROUGHOUT3RIY1.9861.411556986282.910.206090.202690.26634RANDOM30.467
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]
0.03-0.09-0.080.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.59
r_dihedral_angle_4_deg14.812
r_dihedral_angle_3_deg14.156
r_long_range_B_other7.391
r_long_range_B_refined7.389
r_dihedral_angle_1_deg6.803
r_scangle_other4.608
r_mcangle_it3.929
r_mcangle_other3.928
r_scbond_it2.906
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.59
r_dihedral_angle_4_deg14.812
r_dihedral_angle_3_deg14.156
r_long_range_B_other7.391
r_long_range_B_refined7.389
r_dihedral_angle_1_deg6.803
r_scangle_other4.608
r_mcangle_it3.929
r_mcangle_other3.928
r_scbond_it2.906
r_scbond_other2.901
r_mcbond_it2.585
r_mcbond_other2.585
r_angle_refined_deg1.85
r_angle_other_deg1.068
r_chiral_restr0.101
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms121
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing