6ACO

histone lysine desuccinylase Sirt5 in complex with succinyl peptide H2BK120


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6ACE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52950.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate (pH 6.5), 30%(w/v) PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.0138.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.885α = 90
b = 64.877β = 95.92
c = 55.564γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2018-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.9792SSRFBL17U1

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
11.755.2792.30.08915.46.923736
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)
11.71.760.355

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 REPLACEMENTTHROUGHOUT6ACE1.7155.2722645107991.470.163530.160960.217RANDOM29.941
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]
-1.371.121.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.041
r_dihedral_angle_4_deg16.251
r_dihedral_angle_3_deg13.572
r_long_range_B_other8.146
r_long_range_B_refined8.144
r_dihedral_angle_1_deg6.388
r_scangle_other6.304
r_scbond_it4.223
r_scbond_other4.218
r_mcangle_it3.835
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.041
r_dihedral_angle_4_deg16.251
r_dihedral_angle_3_deg13.572
r_long_range_B_other8.146
r_long_range_B_refined8.144
r_dihedral_angle_1_deg6.388
r_scangle_other6.304
r_scbond_it4.223
r_scbond_other4.218
r_mcangle_it3.835
r_mcangle_other3.835
r_angle_other_deg3.742
r_mcbond_it2.862
r_mcbond_other2.839
r_angle_refined_deg2.19
r_chiral_restr0.139
r_bond_refined_d0.026
r_gen_planes_other0.02
r_gen_planes_refined0.013
r_bond_other_d
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 Atoms2123
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms8

Software

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