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The structure of vanin-1: defining the link between metabolic disease, oxidative stress and inflammation
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 PROTEIN 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 coefficient Solvent content 3.89 68.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.941 α = 90 b = 119.941 β = 90 c = 221.887 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADXV 2013-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.25 48.3 99.8 0.14 15.2 14.8 77299
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.37 99.3 1.18 2.7 14.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SIRAS THROUGHOUT NONE 2.25 105.51 73353 3872 99.72 0.19678 0.19548 0.2031 0.22176 0.2294 RANDOM 40.411
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] 0.88 0.88 -1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.705 r_dihedral_angle_4_deg 19.277 r_dihedral_angle_3_deg 13.557 r_dihedral_angle_1_deg 6.679 r_mcangle_it 4.082 r_scbond_it 3.248 r_mcbond_it 2.611 r_mcbond_other 2.611 r_angle_refined_deg 1.252 r_angle_other_deg 0.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.705 r_dihedral_angle_4_deg 19.277 r_dihedral_angle_3_deg 13.557 r_dihedral_angle_1_deg 6.679 r_mcangle_it 4.082 r_scbond_it 3.248 r_mcbond_it 2.611 r_mcbond_other 2.611 r_angle_refined_deg 1.252 r_angle_other_deg 0.832 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 Atoms Number Protein Atoms 7264 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling Auto-Rickshaw phasing