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Crystal structure of E18D DJ-1 with oxidized C106
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P5F pdb entry 1P5F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 1.5 M sodium citrate, 25 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.89 57.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.75 α = 90 b = 74.75 β = 90 c = 74.8 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 110 CCD ADSC QUANTUM 315 BENT CONICAL RH-COATED SI MIRROR 2006-03-14 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) 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 1.2 30 99.8 0.066 32 9.9 75693 75693
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) 1.2 1.24 100 0.64 3.7 9.5 7532
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R pdb entry 1P5F 1.2 30 75606 75606 3779 99.8 0.1225 0.1225 0.1225 0.1552 0.1399 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 10 1402 1621.7
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.119 s_non_zero_chiral_vol 0.09 s_zero_chiral_vol 0.075 s_similar_adp_cmpnt 0.049 s_anti_bump_dis_restr 0.033 s_angle_d 0.03 s_from_restr_planes 0.0292 s_bond_d 0.014 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1458 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection SHELX model building SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling SHELX phasing