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The structure of vanin-1: defining the link between metabolic disease, oxidative stress and inflammation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CYF PDB ENTRY 4CYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 281 CRYSTALLIZATION CONDITIONS: PROTEIN AT 12 MG/ML IN 50 MM BIS-TRIS PH 6.5 WITH 50 MM NACL. RESERVOIR CONDITIONS WERE 21% PEG 1500 WITH 10% (V/V) MALATE-MES-TRIS BUFFER AT PH 6.3. DROPS WERE 200 NL PLUS 200 NL IN SITTING DROP PLATES AT 8C.
Crystal Properties Matthews coefficient Solvent content 3.88 68.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.093 α = 90 b = 120.093 β = 90 c = 221.9 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 ADSC CCD 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 2.3 48.3 99.6 0.15 15.6 14.9 72390
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 2.3 2.42 99.3 1.24 2.6 15.2
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4CYF 2.3 105.62 68703 3638 99.42 0.18765 0.18624 0.1926 0.21444 0.2167 RANDOM 36.863
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] 0.24 0.24 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.508 r_dihedral_angle_4_deg 17.562 r_dihedral_angle_3_deg 12.708 r_dihedral_angle_1_deg 6.551 r_mcangle_it 3.134 r_scbond_it 2.577 r_mcbond_it 1.962 r_mcbond_other 1.959 r_angle_refined_deg 1.24 r_angle_other_deg 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.508 r_dihedral_angle_4_deg 17.562 r_dihedral_angle_3_deg 12.708 r_dihedral_angle_1_deg 6.551 r_mcangle_it 3.134 r_scbond_it 2.577 r_mcbond_it 1.962 r_mcbond_other 1.959 r_angle_refined_deg 1.24 r_angle_other_deg 0.82 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 7267 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 168
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing