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The Crystal Structure of DJ-1 Superfamily Protein Atu0886 from Agrobacterium tumefaciens
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1M Tris 8.5, 1.5M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.78 55.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.411 α = 90 b = 89.411 β = 90 c = 163.486 γ = 90
Symmetry Space Group P 41 21 2
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 SBC-3 Mirrors 2005-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97910 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.7 78.33 99.16 0.093 0.077 51.571 19 73282 73282 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 97.2 0.573 0.506 3.463 9.8 7019
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 1.7 78.33 69187 69187 3659 99.16 0.166 0.166 0.164 0.1647 0.199 0.1668 RANDOM 23.003
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] 0.43 0.43 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.476 r_dihedral_angle_4_deg 23.144 r_dihedral_angle_3_deg 12.426 r_dihedral_angle_1_deg 5.323 r_scangle_it 4.343 r_scbond_it 2.822 r_angle_refined_deg 1.646 r_mcangle_it 1.585 r_mcbond_it 0.989 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.476 r_dihedral_angle_4_deg 23.144 r_dihedral_angle_3_deg 12.426 r_dihedral_angle_1_deg 5.323 r_scangle_it 4.343 r_scbond_it 2.822 r_angle_refined_deg 1.646 r_mcangle_it 1.585 r_mcbond_it 0.989 r_nbtor_refined 0.314 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.194 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.128 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4091 Nucleic Acid Atoms Solvent Atoms 681 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing Coot model building ARP/wARP model building CCP4 phasing