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Atomic resolution structure of human DJ-1, DTT bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P5F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 23-27% PEG 3000, 100 mM HEPES, 200 mM NaCl, 10 mM dithiothreitol (DTT)
Crystal Properties Matthews coefficient Solvent content 3.06 59.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.227 α = 90 b = 75.227 β = 90 c = 75.227 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 bent conical Si, Rh coated 2006-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.15 49 100 0.088 1 16.3 11.1 87636
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.17 99.7 1.667 0.614 1.7 8.4
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 1P5F 1.15 49 83306 4296 99.99 0.11067 0.10971 0.1107 0.12948 0.1306 RANDOM 18.749
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] -0.04 -0.02 -0.04 0.14
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 51.923 r_dihedral_angle_2_deg 34.166 r_dihedral_angle_4_deg 20.794 r_sphericity_bonded 15.704 r_dihedral_angle_3_deg 11.062 r_long_range_B_refined 7.322 r_long_range_B_other 7.32 r_dihedral_angle_1_deg 5.929 r_scangle_other 3.549 r_scbond_it 3.113
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 51.923 r_dihedral_angle_2_deg 34.166 r_dihedral_angle_4_deg 20.794 r_sphericity_bonded 15.704 r_dihedral_angle_3_deg 11.062 r_long_range_B_refined 7.322 r_long_range_B_other 7.32 r_dihedral_angle_1_deg 5.929 r_scangle_other 3.549 r_scbond_it 3.113 r_scbond_other 3.112 r_rigid_bond_restr 2.746 r_mcangle_other 2.589 r_mcangle_it 2.588 r_mcbond_other 1.913 r_mcbond_it 1.905 r_angle_refined_deg 1.675 r_angle_other_deg 1.041 r_chiral_restr 0.117 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1374 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction Aimless data scaling PHASER phasing