6ACP

histone lysine desuccinylase Sirt5 in complex with succinyl peptide H4K91


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52950.1 M BIS-TRIS (pH 5.5), 25% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2344.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.078α = 90
b = 41.267β = 108.37
c = 61.334γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.9793SSRFBL18U1

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
12.358.21990.1498.55.112138
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)
12.32.380.412

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 REPLACEMENTTHROUGHOUT6ACE2.358.211132062398.920.207210.203270.2851RANDOM69.033
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]
-1.271.364.22-3.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.14
r_dihedral_angle_4_deg22.707
r_dihedral_angle_3_deg15.254
r_long_range_B_refined12.132
r_long_range_B_other12.13
r_scangle_other9.43
r_mcangle_it7.936
r_mcangle_other7.933
r_dihedral_angle_1_deg6.643
r_scbond_it6.351
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.14
r_dihedral_angle_4_deg22.707
r_dihedral_angle_3_deg15.254
r_long_range_B_refined12.132
r_long_range_B_other12.13
r_scangle_other9.43
r_mcangle_it7.936
r_mcangle_other7.933
r_dihedral_angle_1_deg6.643
r_scbond_it6.351
r_scbond_other6.348
r_mcbond_it5.561
r_mcbond_other5.56
r_angle_other_deg3.729
r_angle_refined_deg1.664
r_chiral_restr0.095
r_bond_refined_d0.092
r_gen_planes_other0.012
r_gen_planes_refined0.011
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 Atoms2098
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms1

Software

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