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DJ-1 C106S incubated with isatin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SOA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293.15 100mM TRIS-HCl, 200mM sodium citrate, 30% PEG-400, 5mM DTT
Crystal Properties Matthews coefficient Solvent content 3.04 59.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.86 α = 90 b = 74.86 β = 90 c = 74.69 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 2013-04-17 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 1.6 32.4 99.8 0.091 10.2 5 32338
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 1.6 1.69 98.7 0.617 2.4 4.9
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 1SOA 1.6 32.4 30987 1324 99.8 0.14588 0.14484 0.1594 0.17192 0.1857 RANDOM 16.74
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] -0.16 -0.08 -0.16 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.201 r_dihedral_angle_4_deg 18.783 r_dihedral_angle_3_deg 14.607 r_long_range_B_refined 6.879 r_long_range_B_other 6.502 r_dihedral_angle_1_deg 6.304 r_scangle_other 4.588 r_scbond_it 2.906 r_scbond_other 2.904 r_mcangle_other 2.518
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.201 r_dihedral_angle_4_deg 18.783 r_dihedral_angle_3_deg 14.607 r_long_range_B_refined 6.879 r_long_range_B_other 6.502 r_dihedral_angle_1_deg 6.304 r_scangle_other 4.588 r_scbond_it 2.906 r_scbond_other 2.904 r_mcangle_other 2.518 r_mcangle_it 2.51 r_angle_refined_deg 2.026 r_mcbond_it 1.598 r_mcbond_other 1.573 r_angle_other_deg 0.913 r_chiral_restr 0.115 r_bond_refined_d 0.018 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1376 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing