5X16

Sirt6 apo structure


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277.150.1M Sodium citrate tribasic dihydrate pH 5.6, 35% v/v tert-Butanol
Crystal Properties
Matthews coefficientSolvent content
2.4349.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.565α = 90
b = 68.138β = 90
c = 117.314γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CMOSDECTRIS PILATUS3 S 6M2016-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U11.0000SSRFBL19U1

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
11.975095.40.05818.9273.788468-3
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)
11.972.0193.90.4582.1863.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.975022077114993.630.186540.184080.2316RANDOM33.496
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]
-0.4-0.450.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.911
r_dihedral_angle_4_deg16.734
r_dihedral_angle_3_deg13.368
r_long_range_B_refined6.46
r_long_range_B_other6.372
r_dihedral_angle_1_deg5.871
r_scangle_other3.755
r_mcangle_it2.877
r_mcangle_other2.877
r_scbond_it2.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.911
r_dihedral_angle_4_deg16.734
r_dihedral_angle_3_deg13.368
r_long_range_B_refined6.46
r_long_range_B_other6.372
r_dihedral_angle_1_deg5.871
r_scangle_other3.755
r_mcangle_it2.877
r_mcangle_other2.877
r_scbond_it2.29
r_scbond_other2.289
r_mcbond_it1.811
r_mcbond_other1.809
r_angle_refined_deg1.546
r_angle_other_deg0.994
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms2282
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
SCALEPACKdata processing
REFMACmodel building