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Structural insights into thiol stabilization of DJ-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PDV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 293 45% (v/v) polyproylene glycol 400, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 41.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.88 α = 90 b = 41.831 β = 115.79 c = 63.344 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS HTC 2011-03-03
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT
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 1.53 20 93 0.044 19.4 4.9 47218 2
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 1.53 1.61 82.4 0.252 4.7 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1PDV 1.56 20 45524 42954 2318 94.3 0.174 0.172 0.211 0.2195 RANDOM 25.12
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] -0.51 -0.73 1.4 -1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.738 r_dihedral_angle_4_deg 17.019 r_dihedral_angle_3_deg 13.786 r_dihedral_angle_1_deg 12.185 r_scangle_it 7.041 r_scbond_it 4.418 r_mcangle_it 3.194 r_rigid_bond_restr 2.588 r_mcbond_it 1.888 r_angle_refined_deg 1.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.738 r_dihedral_angle_4_deg 17.019 r_dihedral_angle_3_deg 13.786 r_dihedral_angle_1_deg 12.185 r_scangle_it 7.041 r_scbond_it 4.418 r_mcangle_it 3.194 r_rigid_bond_restr 2.588 r_mcbond_it 1.888 r_angle_refined_deg 1.421 r_chiral_restr 0.108 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2777 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling