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Crystal structure of DJ-1 with Zinc(II) bound (crystal I)
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 8 293 100 mM TRIS
20% (v:v) PEG-400
Co-crystal with 500 uM Zn(II)
Crystal Properties Matthews coefficient Solvent content 3.13 60.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.13 α = 90 b = 75.13 β = 90 c = 75.54 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 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 1.75 65.06 100 0.094 18.5 10.6 25307
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 1.75 1.84 100 0.498 4.9 10.8
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 1.75 26.6 24237 1043 99.96 0.14279 0.14161 0.1556 0.17132 0.1782 RANDOM 18.579
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 0.12 0.24 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.46 r_dihedral_angle_4_deg 20.359 r_dihedral_angle_3_deg 11.629 r_dihedral_angle_1_deg 6.272 r_long_range_B_refined 6.261 r_long_range_B_other 5.894 r_scangle_other 3.104 r_scbond_it 1.988 r_scbond_other 1.961 r_angle_refined_deg 1.734
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.46 r_dihedral_angle_4_deg 20.359 r_dihedral_angle_3_deg 11.629 r_dihedral_angle_1_deg 6.272 r_long_range_B_refined 6.261 r_long_range_B_other 5.894 r_scangle_other 3.104 r_scbond_it 1.988 r_scbond_other 1.961 r_angle_refined_deg 1.734 r_mcangle_other 1.491 r_mcangle_it 1.489 r_mcbond_it 0.975 r_mcbond_other 0.929 r_angle_other_deg 0.852 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1375 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOSFLM data reduction PHASER phasing