☰ Navigation Tabs
Crystal structure of DJ-1 in sulfinic acid form (aged crystal)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SOA PDB entry 1SOA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 200 mM sodium citrate
30% (v:v) PEG400
Crystal Properties Matthews coefficient Solvent content 3.09 60.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.76 α = 90 b = 74.76 β = 90 c = 75.03 γ = 120
Symmetry Space Group P 31 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 CCD ADSC QUANTUM 315 2013-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 1.35 64.74 100 0.095 13.2 7 53628
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 1.35 1.42 100 0.313 5.5 7
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 1SOA 1.35 29.7 52067 1525 99.95 0.09852 0.09789 0.1034 0.12012 0.1243 RANDOM 17.646
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] 0.11 0.06 0.11 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.349 r_sphericity_free 24.372 r_dihedral_angle_4_deg 18.921 r_dihedral_angle_3_deg 12.189 r_sphericity_bonded 9.167 r_dihedral_angle_1_deg 5.956 r_rigid_bond_restr 5.146 r_long_range_B_refined 3.992 r_scbond_it 3.489 r_scbond_other 3.479
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.349 r_sphericity_free 24.372 r_dihedral_angle_4_deg 18.921 r_dihedral_angle_3_deg 12.189 r_sphericity_bonded 9.167 r_dihedral_angle_1_deg 5.956 r_rigid_bond_restr 5.146 r_long_range_B_refined 3.992 r_scbond_it 3.489 r_scbond_other 3.479 r_scangle_other 3.448 r_long_range_B_other 3.232 r_mcbond_it 2.344 r_mcangle_other 2.088 r_angle_refined_deg 2.073 r_mcbond_other 2.026 r_mcangle_it 1.94 r_angle_other_deg 0.904 r_chiral_restr 0.129 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1377 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement