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Crystal structure of human DJ-1 with a natural modification on Cys-106
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, HANGING DROP 7.5 298 0.1M HEPES-Na, 1.5M Tri-sodium citrate dihydrate pH=7.5
Crystal Properties Matthews coefficient Solvent content 3.06 59.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.715 α = 90 b = 74.715 β = 90 c = 74.807 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 MARMOSAIC 225 mm CCD mirrors 2014-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.35 50 99.8 0.055 0.058 0.018 10.1 10.9 53266
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.37 100 1.202 1.264 0.387 0.742 10.6
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 1.35 32.4 48665 2569 96.06 0.1133 0.112 0.112 0.1388 0.1394 RANDOM 19.295
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] 0.07 0.04 0.07 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.903 r_dihedral_angle_4_deg 21.57 r_sphericity_free 17.573 r_sphericity_bonded 17.268 r_dihedral_angle_3_deg 11.783 r_dihedral_angle_1_deg 6.162 r_rigid_bond_restr 5.165 r_angle_refined_deg 1.528 r_angle_other_deg 1.099 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.903 r_dihedral_angle_4_deg 21.57 r_sphericity_free 17.573 r_sphericity_bonded 17.268 r_dihedral_angle_3_deg 11.783 r_dihedral_angle_1_deg 6.162 r_rigid_bond_restr 5.165 r_angle_refined_deg 1.528 r_angle_other_deg 1.099 r_chiral_restr 0.1 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1379 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing