4CYF

The structure of vanin-1: defining the link between metabolic disease, oxidative stress and inflammation


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5PROTEIN WAS AT 12 MG/ML IN 50 MM BIS-TRIS PH 6.5 WITH 50 MM NACL. THE RESERVOIR WAS 21% PEG 1500 WITH 10% (V/V) MALATE-MES-TRIS BUFFER AT PH 6.3. 200 NL PLUS 200 NL DROPS IN SITTING DROP PLATES.
Crystal Properties
Matthews coefficientSolvent content
3.8968.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.941α = 90
b = 119.941β = 90
c = 221.887γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADXV2013-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX2Australian SynchrotronMX2

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
12.2548.399.80.1415.214.877299
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)
12.252.3799.31.182.714.5

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 DIFFRACTIONSIRASTHROUGHOUTNONE2.25105.5173353387299.720.196780.195480.22176RANDOM40.411
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]
0.880.88-1.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.705
r_dihedral_angle_4_deg19.277
r_dihedral_angle_3_deg13.557
r_dihedral_angle_1_deg6.679
r_mcangle_it4.082
r_scbond_it3.248
r_mcbond_it2.611
r_mcbond_other2.611
r_angle_refined_deg1.252
r_angle_other_deg0.832
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.705
r_dihedral_angle_4_deg19.277
r_dihedral_angle_3_deg13.557
r_dihedral_angle_1_deg6.679
r_mcangle_it4.082
r_scbond_it3.248
r_mcbond_it2.611
r_mcbond_other2.611
r_angle_refined_deg1.252
r_angle_other_deg0.832
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.003
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7264
Nucleic Acid Atoms
Solvent Atoms240
Heterogen Atoms112

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
Auto-Rickshawphasing